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PubMed1979

Deoxyribonucleic acid binding studies on several new anthracycline antitumor antibiotics. Sequence preference and structure--activity relationships of marcellomycin and its analogues as compared to adriamycin.

The deoxyribonucleic acid (DNA) binding characteristics of adriamycin and several new anthracycline glycosides, including marcellomycin, aclacinomycin, rudolfomycin, musettamycin, and pyrromycin, have been studied. The fluorescence spectra were determined for all six anthracyclines, and the fluorescence quenching effects caused by interactions with the natural DNAs poly(dAdT)--poly(dAdT) and poly(dGdC) were characterized. Binding parameters were determined by Scatchard analyses of results obtained by spectrofluorometric titrations of anthracyclines with DNA. Consistent with earlier structure--activity relationship studies of nucleic acid synthesis inhibitory effects, the results demonstrate a correlation between the length of the glycosidic side chain and DNA binding affinity. In addition, the sugar residue 2-deoxyfucose appears to confer greater DNA binding ability than do the sugars rednosamine and cinerulose when present in the terminal position of the glycosidic side chain, also in agreement with earlier studies. The sequence preference of anthracycline--DNA interaction has been examined by using DNAs of varying GC content, including the naturally occurring calf thymus DNA (43% GC), Clostridium perfringens DNA (28% GC), and Micrococcus luteus DNA (72% GC) and the synthetic double-stranded copolymers poly(dGdC)--poly(dGdC) and poly(dAdT)--POLY(DAdT). The results demonstrate that although adriamycin shows an absolute requirement for GC sequences for DNA binding, marcellomycin and its analogues showed no such sequence requirement. Furthermore, an AT preference for DNA binding was demonstrated with marcellomycin and its analogues.

Aclarubicin↗

PubMed2026

Evolutionary dynamics of the chloroplast genome in Abutilon (Malvoideae, Malvaceae).

The genus Abutilon Mill. (Malvaceae) comprises approximately 178 species distributed across tropical and subtropical regions, many of which hold significant ornamental, economic, and medicinal value; yet its taxonomic classification remains challenging. In this study, six species were sequenced from herbarium specimens, and the chloroplast (cp.) genomes of ten additional species were assembled de novo from publicly available raw data. Three previously reported cp. genomes were also incorporated to characterise cp. genome structure, identify polymorphic loci, and perform phylogenetic analyses. The cp. genomes ranged from 159,458 to 160,454 bp and exhibited the typical quadripartite structure, with each genome containing 112 unique genes (78 protein-coding, 30 tRNA, and 4 rRNA) that showed conserved content and organisation. These genomes exhibited high similarity in GC content, inverted repeat boundaries, relative synonymous codon usage, amino acid frequencies, and substitution patterns. However, notable variation was observed in the total number of simple sequence repeats, ranging from 70 to 97 per genome. Selection analyses indicated predominant purifying selection, with evidence of episodic positive selection detected in rpoC2, rbcL, and ycf1. Two codons in rbcL were clade-specific and provided phylogenetic signal distinguishing Australian and Old World pantropical species. Nucleotide diversity analysis identified six highly polymorphic intergenic spacers (trnH-psbA, rps19-rpl2, psbT-pbf1, psaC-ndhD, trnR-atpA, and ndhJ-ndhK) that may be suitable for taxonomic studies. The phylogeny from maximum likelihood (ML) and Bayesian inference (BI) resolved two major clades: one comprising an exclusively Australian lineage occurring predominantly in arid and semi-arid environments, and the other a pantropical lineage spanning multiple continents. Abutilon grandifolium was recovered as sister to the remaining sampled Abutilon taxa in both ML and BI analyses, although no biogeographic origin inference can be drawn from this placement pending broader taxon sampling and integration of nuclear genomic data. These findings provide insights into the evolutionary dynamics of the cp. genome in Abutilon and offer a foundational genomic framework for refining Abutilon taxonomy.

Genome, Chloroplast↗

PubMed1979

[Characteristics of DNA in vegetative specimens of Bursaria truncatella].

DNA from Bursaria truncatella was isolated and purified by conventional methods. The DNA base content was calculated from both centrifugation in CsCl and melting. The GC-content is 24%. In CsCl density gradient 3H-DNA is banded as a single peak at a range 1.682--1.688 g/cm3 with the maximum at 1.684 g/cm3. The Tm in 0.12 M FB (pH 6.8) was 79 degrees C. About 50% of DNA seems to be represented by highly repetitive sequences, another 50% being made of single-copy sequences (a preliminary data on DNA-DNA reassotiation kinetics). For the estimation of the molecular weight of DNA, the cells were lysed immediately before the centrifugation, at the surface of the alkaline isokinetic sucrose gradient solution. Two components of DNA were detected with molecular weights 10-10(6) and 100-10(6) daltons. It is likely that these two components belong to the macronuclear DNA, because according to cytophotometrical evidence the DNA content in the macronucleus of B. truncatella is 2500 times as much as that in its micronucleus.

Animals↗

PubMedDate not supplied

[Effect of dexamethasone and arecoline on the 5-methylcytosine and pyrimidine blocks in the DNA of certain sections of the brain, the liver and the spleen of rats].

In DNA of rat brain and liver tissues content of 5-methylcytosine increased by about 25 percent after dexamethasone administration; arecholine decreased content of 5-methylcytosine by about 20 percent. No other essential changes (GC content, amount of different pyrimidine isoplits) were found in these DNA. These data suggested that changes in 5-methylcytosine content in DNA studied were due to difference in DNA methylation rather than to alteration in DNA molecular population. The changes in DNA methylation, induced by the hormone or the alkaloid, were tissue-specific (brain, liver but not spleen). The level of DNA methylation was different in various parts of brain and correlated with the functional activity of the corresponding cells or genes. The alterations in DNA methylation, induced by the hormone or by the alkaloid, corresponded to changes in RNA synthesis. Thus, DNA methylation may be one of possible control mechanisms of transcription.

Animals↗

PubMed2025

GCfix: a fast and accurate fragment length-specific method for correcting GC bias in cell-free DNA.

MOTIVATION: Cell-free DNA (cfDNA) analysis has wide-ranging clinical applications due to its noninvasive nature. However, cfDNA fragmentomics and copy number analysis can be complicated by GC bias. There is a lack of GC correction software based on rigorous cfDNA GC bias analysis. Furthermore, there is no standardized metric for comparing GC bias correction methods across large sample sets, nor a rigorous experiment setup to demonstrate their effectiveness on cfDNA data at various coverage levels. RESULTS: We present GCfix, a method for robust GC bias correction in cfDNA data across diverse coverages. Developed following an in-depth analysis of cfDNA GC bias at the region and fragment length levels, GCfix is both fast and accurate. It works on all reference genomes and generates correction factors, tagged BAM files, and corrected coverage tracks. We also introduce two orthogonal performance metrics for (i) comparing the fragment count density distribution of GC content between expected and corrected samples, and (ii) evaluating coverage profile improvement post-correction. GCfix outperforms existing cfDNA GC bias correction methods on these metrics. AVAILABILITY AND IMPLEMENTATION: GCfix software and code for reproducing the figures are publicly accessible on GitHub: https://github.com/Rafeed-bot/GCfix_Software.

Software↗

PubMedDate not supplied

[Isolation and characteristics of 2 transcribing families of pigeon-genome repetitive sequences].

From pigeon DNA two families of repeats have been isolated: one (frequency of repetitions 30--40 times per haploid genome) actively transcribing and the second (frequency of repetitions 2000--2800 times) weakly transcribing in erythroid cells. The reassociation kinetics, GC-content and size of isolated repeats were investigated. Actively transcribing repeats (average length of 350 nucleotides) contain about 55% GC-nucleotides and alternate in the genome with AT-rich sequences of the unique type. Comparison of isolated families of repeats revealed differences in the structure and posttranscriptional fate of RNA transcribed from them.

Animals↗

PubMedDate not supplied

[Nucleotide makeup of the DNA of thermophilic bacteria of the genus Thermus].

The nucleotide composition of DNA was determined in extreme thermophilic and obligate thermophilic nonsporeforming bacteria belonging to a new genus Thermus. The GC content (in mol%) in the DNA of exteme thermophilic bacteria varied from 65.3 to 70.8 per cent depending on the strain. The amount of GC (in mol% in the DNA of obligate thermophilic and extreme thermophilic bacteria of the Thermus genus was higher than that in the DNA of sporeforming obligate thermophilic Bac. coagulans. Bac. circulans and Bac. stearothermophilus.

Cytosine Nucleotides↗

PubMed1978

[Tissue-specific decrease and change in the character of DNA methylation in cattle with aging].

The content of 5-methylcytosine (m5C) in DNA of different cow organs is found to decrease in ontogenesis. No other age changes were found in DNA structure and molecular population (GC content, the content of different in the length and the base composition pyrimidine clusters, hyperchromicity value etc.). It is suggested that the age tissue-specific decrease of the m5C content is due to a decrease of the level of DNA methylation, which takes place in heart, kidneys, spleen and brain DNAs and is not observed in lungs. Maximal level of DNA methylation was observed at embryogenesis, when the m5C content in heart DNA decreases (from 1.8 to 1.4 mol. %), then it remains stable up to 1 year old and then sharply decreases with age and reaches 0.94 mol. % at the age of 10 years. The m5C content in liver DNA decreases (from 1.6 to 1.2 mol. %) at the end of embryogenesis and then it does not change. A pronounced decrease of the m5C content was observed in DNAs of cerebral hemispheres, cerebellum, hyppocampus, neurohypophysis and thymus. The decrease of m5C content in thymus DNA is non-random, it concerns only Pu-m5C-Pu, but not long pyrimidine clusters Pu-Pyn-Pu (n greater than or equal to 2). Tissue-specific decrease and the change in pattern of DNA methylation observed are suggested to be a possible mechanism for the age change (distortion) of transcription and cell functioning.

Aging↗

PubMed1978

Co-replication of satellite DNA of Chironomus melanotus with mainband DNA during polytenization.

The DNAs of five Chironomus species, C. plumosus, C. nuditarsis, C. thummi thummi, C. melanotus, and Camptochironomus pallidivittatus, were investigated in analytical neutral isopycnic CsCl density gradients. DNA was isolated both from larval brains ("diploid-DNA") and salivary glands ("polytene-DNA"). The buoyant densities of mainband DNAs were 1.692 g/cm3, with the exception of C. melanotus whose mainband had a density of 1.693 g/cm3. The densities correspond to a calculated GC content of 33% and 34% respectively. Only in C. melanotus was the DNA clearly resolved into mainband DNA and two distinct satellite shoulders: Satellite I, with a buoyant density of 1.684 g/cm3 (25% GC, calculated) and satellite II of 1.679 g/cm3 (19% GC, calculated). The two satellites comprise 15% of the total DNA in the "diploid-DNA"' and they also occur in the "polytene-DNA", where they make up 11%. The results are discussed in the general context of under- and overreplication in polyploid and polytene cells.

Animals↗

PubMed2026

[Genetic diversity analysis of Forsythia suspensa germplasm resources in Shanxi based on phenotypic traits and SNP molecular markers].

This study aimed to clarify the degree of fruit phenotypic variation and the characteristics of genetic diversity, population structure, and genetic differentiation of Forsythia suspensa resources in Shanxi, providing an important basis for germplasm conservation and breeding of superior varieties. A total of 46 F. suspensa fruits were collected, and 12 agronomic traits were measured and analyzed. The population genetic structure and genetic diversity of F. suspensa germplasm were evaluated using simplified genome sequencing technology. For the five quality traits of the 46 fruits, the Shannon-Wiener index ranged from 0.631 to 1.074, and the Simpson index ranged from 0.379 to 0.560. The seven quantitative traits exhibited abundant genetic variation, with coefficients of variation ranging from 9.764%(fruit shape index) to 45.494%(forsythin content). Principal component analysis reduced the 12 phenotypic traits to four factors, with a cumulative variance contribution of 74.547%. Sequencing data showed mean Q20 and Q30 values of 98.13% and 94.33%, respectively, with an average GC content of 35.95%. After filtering, a total of 12 347 327 high-quality single nucleotide polymorphism(SNP) loci were obtained. Based on these high-quality SNPs, principal component analysis, population structure analysis, and phylogenetic tree construction were carried out. The 46 germplasm resources were divided into four groups; however, grouping showed little relationship with geographic origin, and intermixing occurred among regions. Mantel test revealed a significant but weak positive correlation between phenotypic and genetic distances(r=0.159, P=0.001). At the molecular level, the four groups exhibited moderate genetic diversity overall, and the genetic differentiation index among populations ranged from 0.027 to 0.084, indicating low to moderate differentiation. The rich genetic diversity of the main phenotypic traits provides a solid material basis for screening superior germplasm and genetic breeding of F. suspensa.

Forsythia↗

PubMed1979

[Age- and tissue-specific differences in intragenome distribution of 5'-methylcytosine in cow's DNA].

In aged animals the content of 5'-methylcytosine (m5C) in total thymus DNA (1,29 mol.%) and heart muscle (1,10 mol.%) is decreased by 30 and 40%, respectively as compared to that in the 8-months-old embryos. No differences in the GC-content and reassociation kinetics of these DNAs have been revealed. Consequently, the age differences in the m5C content are caused by the decrease in DNA methylation upon ageing. The degree of DNA methylation in various organs (thymus, heart) is different. Upon ageing the degree of genome methylation is decreased and the pattern of methylation is changed: the m5C content is decreased in the repeated sequences and remains practically unchanged in the unique ones. The level of methylation in thymus DNA of moderately (C0t = 4--400) and highly (C0t less than 4) repeated sequences is thereby decreased almost in the same degree. In heart DNA of aged cows the hypomethylation of highly repeated sequences is more pronounced as compared to the moderately repeated ones. The age- and tissue-specific decrease of DNA methylation is regarded as a possible mechanism responsible for the decrease of transcription and functional activity of the cells upon ageing.

Aging↗

PubMed2026

Draft genome sequence data of Streptomyces antibioticus SCBA4 isolated from the Soils of Surigao del Sur, Philippines.

The draft genome of Streptomyces antibioticus SCBA4 isolated from the soils of Surigao del Sur, Philippines is reported here. S. antibioticus is a member of the phylum Actinomycetota, a diverse group of Gram positive, high G+C content bacteria well known for their production of a variety of bioactive compounds. Sequencing using the Illumina NovaSeq 6000 platform yielded a 8,616,999 bp genome across 36 contigs with 7621 coding sequences, 87 tRNA, and 1 tmRNA. Consistent with the members of the same phylum, the GC content was 71.83% and was found to contain putative gene clusters of secondary metabolites such as NRPs, terpenes and polyketides. The genome sequence has been deposited at NCBI under the accession number JBSWZT020000000.

Actinobacteria↗

PubMed1979

[Intragenome distribution of 5-methyl cytosine and reassociation kinetics of cow blood lymphocyte DNA under normal conditions and in chronic lymphoid leukemia].

The DNA from cow blood lymphocytes is methylated in a varying degree: the maximal content of 5-methyl cytosine (2,3 mol%) is found in the "instantly" renaturating sequences (Cot lett than 10(-4)), a relatively large amount (1,4 mol%)--in moderately repeated sequences (Cot = 10(-4)--400) and the minimal amount (0,9 mol%) in the unique sequences (Cot greater than 400). In their reassociation kinetics, GC-content and other physico-chemical properties the blood lymphocyte DNA of the controls and of animals with chronic lymphoid leukemia appear to be similar. Consequently, the genome organization of leukemic animals does not change significantly; a considerable decrease of 5-methyl cytosine of lymphocyte DNA in lymphoid leukemia parallels the decrease of genome methylation in the leukemic cells. This decrease does not affect the unique sequences, but involves all types of repeated sequences (moderately and frequently repeated ones and palindromes). It is assumed that the specific disturbances in genome methylation under lymphoid leukemia may be a cause of transcription deficiences and cell transformations.

Animals↗

PubMed1979

[Mitochondrial ribosomes of the phytoflagellata Astasia longa].

The physico-chemical properties of ribosomes and rRNA isolated from the mitochondria of the phytoflagellata Astasia longa were studied. It was shown that the mitochondrial ribosomes of A. longa have the sedimentation coefficient of 81S (those of the cytoplasm-82S); upon a decrease of Mg2+ concentration in the medium they dissociate into subparticles with sedimentation coefficients of 60 and 45S. The relative protein content in the mitochondrial ribosomes of A. longa is equal to 42% (rho = 1,60 g/cm3), that of cytoplasmic ribosomes-49%. The molecular weights of mitochondrial rRNA are equal to 1,05 . 10(6) and 0,71 . 10(6) and differ from those for cytoplasmic rRNA (1,32 . 10(6) and 0,94 . 10(6)). It was shown that the GC-content in mitochondrial rRNA is equal to 32,0 mol. %, that in cytoplasmic rRNA-55,9 mol. %. Thus, the mitochondrial ribosomes of A. longa differ in some of their properties from both procaryotic and eucaryotic ribosomes and are probably related to a special type of mitochondrial ribosomes.

Animals↗

PubMed1979

[Changes in DNA methylation in alfalfa plants infected with Cuscuta and tissue differences in DNA methylation of the parasite plants].

The tissue-specific differences in the 5-methylcytosine (m5C) content in total DNA of the parasite plant Cuscuta reflexa have been found: DNA from apical parts of the plant is less methylated (m5C = 4,2 mol %) as compared to the DNA from haustoria and posthaustorial regions (m5C = 5,4 mol %). The base compositions of total DNA preparations from C. reflexa grown on various hosts are similar. The m5C amount in stem DNA of the alfalfa plant infected with C. reflexa is by approximately 25% higher than that in the non-infected plant DNA. The GC content in alfalfa DNA does not change as a result of infection. Thus, the parasite induces the hypermethylation of DNA in the host plant. It is assumed that the changes in DNA methylation induced by the parasite plant may play a regulatory role and may cause changes in transcription and replication of host DNA.

Cytosine↗

PubMed2026

Clinical performance of the urine-based TERT promoter AbsoluteQ Digital PCR for non-invasive detection of bladder cancer.

Bladder cancer (BC) is the ninth most common cancer worldwide, with urothelial carcinoma accounting for approximately 90% of all cases and presenting predominantly as non-muscle-invasive disease. Due to its high recurrence rate and the need for long-term surveillance, BC is associated with the highest lifetime treatment costs per patient among all cancers, making its effective management a significant clinical and economic challenge. The most frequently identified variants in the TERT gene promoter are c.-124C>T (C228T) and c.-146C>T (C250T), located within a region characterized by high guanine-cytosine (GC) content, which makes amplification challenging. We aimed to validate the AbsoluteQ Digital PCR assay for the detection of urine-based TERT promoter variants for the diagnosis of urothelial bladder cancer and to assess its diagnostic performance in comparison with standard methods. Urine samples were collected from patients with histopathologically confirmed bladder cancer (n = 58) and compared with a control group (n = 55). The C228T and C250T variants were tested using the AbsoluteQ Digital PCR assay. Sensitivity, specificity, and predictive values were calculated to evaluate the performance of the assessed method. The AbsoluteQ Digital PCR demonstrated superior diagnostic performance compared to conventional Sanger sequencing for detecting TERT promoter variants, achieving a sensitivity of 89.65% (95% CI: 78.16-95.72) and a specificity of 100% (95% CI: 91.87-100), with no false positives observed. Given its robustness and clinical relevance, AbsoluteQ Digital PCR is emerging as a promising tool for non-invasive molecular diagnostics targeting TERT promoter variants.

Humans↗

PubMed2026

Exploring the Mitochondrial Genomes of Phoebe Species (Lauraceae): Structural Dynamics and Functional Conservation.

Plant mitochondrial genomes (mitogenomes) vary markedly in size and architecture despite generally slow rates of sequence evolution. Phoebe is an ecologically and economically valuable genus of Lauraceae, yet its mitogenome diversity remains poorly characterized. In this study, we newly sequenced, assembled, and annotated the mitogenomes of three nationally protected Class II wild plants (P. bournei, P. chekiangensis, P. zhennan) from China and compared their mitogenomic characteristics. The three assemblies were resolved into representative circular configurations ranging from 808 to 864 kb, with similar GC contents and conserved protein-coding capacity. Each mitogenome contained distinct 41 protein-coding genes, 27-28 transfer RNAs, and three ribosomal RNAs. Synteny analysis revealed extensive changes in homologous-block order and orientation despite substantial sequence homology among the three species. Abundant repeats occurred predominantly in noncoding regions, while plastid-derived fragments documented historical intracellular DNA transfer. The three species exhibited similar codon usage and predicted RNA-editing patterns, whereas low synonymous divergence limited inference from pairwise ratios. Phylogenetic analysis based on mitochondrial protein-coding genes recovered Phoebe as a well-supported monophyletic lineage. These results reveal substantial structural divergence accompanied by conserved nucleotide composition and coding capacity, providing valuable data for further understanding the evolutionary variation of plant mitogenomes of Phoebe and the Lauraceae.

Phoebe↗

PubMed2026

Unveiling the Probiotic Properties of Lacticaseibacillus paracasei UFTM 2.9 Through Probiogenomic Analysis.

Lactic acid bacteria (LAB) comprise a group of Gram-positive bacteria with biotechnological applications. LAB, including Lacticaseibacillus spp., are recognized as potential probiotics due to their ability to confer benefits to the host. Here we employ probiogenomic and in vitro analyses to characterize the probiotic potential of Lc. paracasei UFTM 2.9, a LAB that previously demonstrated probiotic properties in vitro. The draft genome of Lc. paracasei UFTM 2.9 comprises 127 contigs, totaling 3 216 252 base pairs, with a GC content of 46.20%. The bacteria showed metabolic versatility, growing in five carbon sources. A total of 170 genes potentially associated with probiotic characteristics were identified, with functions linked to stress resistance (n = 106), adhesion (n = 12), biosynthesis of vitamins (n = 10), and others. No virulence genes or CRISPR elements were detected, and two phages were identified in Lc. paracasei UFTM 2.9. Gene clusters encoding bacteriocins were detected and confirmed in vitro. Lc. paracasei UFTM 2.9 inhibited all indicator bacteria tested (n = 12), including strains of Listeria innocua, Staphylococcus aureus, Streptococcus agalactiae, and Escherichia coli. The results indicate the potential use of Lc. paracasei UFTM 2.9 as a probiotic, considering its genetic potential to express traits of interest and survive in the gastrointestinal tract (GIT).

Probiotics↗