Characterisation of the Novel HLA-DPB1*1784:01 Allele by Sequencing-Based Typing.
HLA-DPB1*1784:01 differs from HLA-DPB1*514:01 by one nucleotide substitution in codon 57 in exon 2.
Humans↗
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Newly Developed Structure-Based Methods Do Not Outperform Standard Sequence-Based Methods for Large-Scale Phylogenomics.
Recent developments in protein structure prediction have allowed the use of this previously limited source of information at genome-wide scales. It has been proposed that the use of structural information may offer advantages over sequences in phylogenetic reconstruction, due to their slower rate of evolution and direct correlation to function. Here, we examined how recently developed methods for structure-based homology search and tree reconstruction compare with current state-of-the-art sequence-based methods in reconstructing genome-wide collections of gene phylogenies (i.e. phylomes). While structure-based methods can be useful in specific scenarios, we found that their current performance does not justify using the newly developed structure-based methods as a default choice in large-scale phylogenetic studies. On the one hand, the best performing sequence-based tree reconstruction methods still outperform structure-based methods for this task. On the other hand, structure-based homology detection methods provide larger lists of candidate homologs, as previously reported. However, this comes at the expense of missing hits identified by sequence-based methods, as well as providing sets of homolog candidates with higher fractions of false positives. These insights help to guide the use of structural data in comparative genomics and highlight the need to continue improving structure-based approaches. Our pipeline is fully reproducible and has been implemented in a Snakemake workflow. This will facilitate a continuous assessment of future improvements of structure-based tools in the AlphaFold era.
Phylogeny↗
On the base sequence of the promoter of Alzheimer's disease amyloid A4 precursor gene in transcription initiation.
The base sequence of a specific DNA region of the APP gene identified as the promoter was analyzed by means of the quantity Sr corresponding to superdelocalizability of oxygen ion of each phosphate for the ten DNA dimer units (XY/Y' X') and the six [(XY/Y'X')+H+] complexes. The base sequence of the -35 signal was determined to be 5'-CAGCTG-3' (-49 to -44). On the other hand, the base sequence of the -10 signal was found several ones. Therefore, transcription is to initiate at multiple sites. The mechanisum how RNA polymerases can recognize each transcription site, was proposed. The result explains fairly well some characteristics of the promoter of the APP gene experimentally found so far.
Alzheimer Disease↗
Comparison of the base-sequence complexities of polysomal and nuclear RNAs in growing Friend erythroleukemia cells.
The base-sequence complexities of polysomal poly(A)+ RNA, nuclear poly(A)+ RNA, and total nuclear RNA from Friend erythroleukemia cells in logarithmic phase of growth were determined by measuring the proportion of labeled unique mouse DNA sequences which formed hybrids when incubated with a vast excess of each RNA. It was estimated that the RNAs had been transcribed from 1.8, 7.6, and 8.3%, respectively, of the haploid mouse genome. Although these estimates for polysomal and nuclear poly(A)+ RNAs were 2.5 times greater than those previously determined by analysis of the kinetics of the hybridization reactions between the RNAs and the cDNAs transcribed from them, they confirmed that the base-sequence complexity of nuclear poly(A)+ RNA in these cells is at least four times greater than that of polysomal poly(A)+ RNA.
Base Sequence↗
Base and base sequence specificity of the binding of 4-hydroxyaminoquinoline 1-oxide to DNA.
Synthetic and natural DNAs we;e reacted with 4-hydroxyaminoquinoline 1-oxide (4-HAQO) in an in vitro enzyme system. The amount of 4-HAQO bound to DNA varied significantly depending on the DNA used. The base sequence as well as the base composition affected the binding. Optical melting profiles of 4-HAQO-modified DNAs were examined. Decrease in the melting temperature and broadening of the transition width were commonly observed. Melting fine structure of lambda-phage DNA became less clear according to the modification. The shape of the melting curves of synthetic polynucleotides was little affected by binding, which suggests that the binding sites are distributed randomly along a DNA molecule. Binding of 4-HAQO to a purine base may distort the secondary structure of neighboring base pairs in a DNA molecule. Degree of the distortion can be estimated as a free energy increment associated with the binding. It was found that the free energy increment differs considerably among the polynucleotides with different base sequences.
4-Hydroxyaminoquinoline-1-oxide↗
Diagnostic yield of exome sequencing-based copy number variation analysis in Mendelian disorders: a clinical application.
Next-generation sequencing (NGS) coupled with bioinformatic tools has revolutionized the detection of copy number variations (CNVs), which are implicated in the emergence of Mendelian disorders. In this study, we evaluated the diagnostic yield of exome sequencing-based CNV analysis in 449 patients with suspected Mendelian disorders. We aimed to assess the diagnostic yield of this recently utilized method and expand the clinical spectrum of intragenic CNVs. The cohort underwent whole exome sequencing (WES) and clinical exome sequencing (CES). Using GATK-gCNV, we identified 12 pathogenic CNVs that correlated with their clinical findings and resulting in a diagnostic yield of 2.67%. Importantly, the study emphasizes the role of CNVs in the etiology of Mendelian disorders and highlights the value of exome sequencing-based CNV analysis in routine diagnostic processes.
Humans↗
Platinum - dimethylsulphoxide as a specific nucleic acid reagent for base sequence determination by electron microscopy.
The reaction of platinum (II) - dimethylsulphoxide complex with the bases of the nucleic acids were investigated with a new towards their use as heavy atom markers for base sequence determination by electron microscopy. Both at pH 6.0 and pH 7.5 one platinum atom was bound simultaneously to the pyrimidines and two to adenine, while at the lower pH one platinum, and at the higher pH, two platinum atoms were bound to guanine. The stain therefore appears to be useful to determine the guanine and adenine sequence in single strands of RNA and DNA. Where complementary strands are available the complete sequence determination of all four bases should be possible.
Base Sequence↗
Base sequence complexity of the stable RNA species of Drosophila melanogaster.
The base sequence complexity of Drosophila transfer RNA (tRNA), 5S RNA, and 18S + 28S ribosomal RNA was determined by analyzing the kinetics of RNA-DNA hybridization on membrane filters. We find that Drosophila tRNA is made up from about 59 basic nucleotide sequences distinguishable by hybridization, suggesting that many of the 99 tRNA species resolved by reverse phase chromatography (RPC-5) are homogenic. In contrast 5S RNA was found to contain a single family of sequences. Either 18S ribosomal RNA (rRNA) alone, or 18S + 28S rRNA together, behaved kinetically as two sequence families, and the possible basis for this unexpected result is discussed.
Animals↗
Electron microscope study of the base sequence homology between simian virus 40 and human papovavirus BK.
The base sequence homology between the genomes of simian virus 40 (SV40) and human papovavirus BK (BKV) was studied by the heteroduplex method of Ferguson and Davis (J. Mol. Biol. 94:135-149, 1975). When mounted for microscopy in 30% formamide (Tm-35 degrees C), BKV/SV40 heteroduplexes were an average of 92% double-stranded and contained only two small nonhomologous regions that mapped near the junctions between the early and late regions of the SV40 Genome. At higher formamide concentrations, the fraction of duplex DNA in the BKV/SV40 heteroduplexes decreased, indicating significant base mismatching in the homologous regions. The strongest regions of homology were located in the late region.
BK Virus↗
GBSC: graph-based sequence clustering method for similar short tandem repeats in protein sequences.
MOTIVATION: Short tandem repeats (STRs) are abundant in protein sequences and play important role in determining their structures and functions. Strikingly, the unusual compositional characteristics of tandem repeats break classical sequence analysis tools. RESULTS: Here, we establish the first algorithm to effectively identify and cluster STRs: Graph-Based Sequence Clustering (GBSC) features linear time complexity, and clusters protein sequence fragments based on their STRs, while allowing for insertions and mutations and supporting the analysis of imperfect or cryptic repeats. Due to its computational efficacy, our algorithm can be used to systematically scan for patterns in large datasets. We compare our method both to state-of-the-art methods for identifying STRs in proteins and alternative clustering approaches. Unlike existing STR analysis methods, GBSC clusters repeat patterns rather than raw sequences, operating at the level of structural repeat identity, while tolerating biological variations and preventing erroneous merging of structurally and functionally distinct motifs. Whereas functional annotation is typically only available at the protein level, the functions of individual STRs and sequences of adjacent STRs remain largely unknown. On a challenging use case we here demonstrate and discuss how our method can be used to associate previously unannotated repetitive protein fragments with similar ones, allowing the transfer of annotation by similarity. For the first time, GBSC offers a tool that systematically extends this fundamental bioinformatics principle to low-complexity regions across large datasets. AVAILABILITY AND IMPLEMENTATION: GBSC is available at GitHub https://github.com/patryk-jarnot/GBSC and https://doi.org/10.5281/zenodo.18965247. The data and scripts to reproduce the analysis are available at https://doi.org/10.5281/zenodo.16906653.
Microsatellite Repeats↗
Evolutionary relationships of the primate papovaviruses: base sequence homology among the genomes of simian virus 40, stump-tailed macaque virus, and SA12 virus.
Physical maps of the genomes of the two newly discovered primate papovaviruses, SA12 and stump-tailed macaque virus (STMV), were generated by restriction endonuclease analysis. The base sequence homologies among the genomes of SA12, stump-tailed macaque virus, and simian virus 40 (SV40) were studied by heteroduplex analysis. Heteroduplexes between SA12 and SV40 DNAs and stump-tailed macaque virus and SV40 DNAs were constructed and mounted for electron microscopy in various amounts of formamide to achieve a range of effective temperatures. At each effective temperature, the regions of duplex DNA in the heteroduplexes were measured and localized on the SV40 physical and functional maps. By analyzing the data from this study and rom our previous study (N. Newell, C. J. Lai, G. Khoury, and T. J. Kelly Jr., J. Virol. 25:193-201, 1978) on the base sequence homology between the genomes of BK virus and SV40, some general conclusions have been drawn concerning the evolutionary relationships among the genomes of the primate papovaviruses. The extent of homology among the viral genomes does not reflect the phylogenetic relationships of their hosts. At comparable effective temperatures Tm - 33 degrees C), the heteroduplexes between the DNAs of BK virus and SV40 contained the largest amount of duplex (about 90%). The heteroduplexes made between SA12 and SV40 DNAs were slightly less homologous, containing about 80% duplex. The heteroduplexes made between SV40 and stump-tailed macaque virus DNAs were only 20% duplex under the same conditions. When the various heteroduplexes were mounted for microscopy at effective temperatures greater than Tm - 33 degrees C, the fraction of the duplex DNA decreased in each case, indicating the existence of considerable base mismatching in the homologous regions. When specific coding or noncoding regions of the viral genomes were compared, the data indicated that the extent of sequence divergence differed markedly from one region to another. In all the heteroduplexes studied, there were two regions, located near the junctions between early and late regions on the SV40 map, which were essentially nonhomologous. All of the heteroduplexes studied showed significantly greater homology in the late region than in early region. Within the late region, the sequences coding for the major capsid polypeptide, VP1, were the most highly conserved.
Base Sequence↗
Wastewater-based sequencing of respiratory syncytial virus to investigate lineage dynamics and antigenic site mutations: a retrospective genomic epidemiology study.
BACKGROUND: Respiratory syncytial virus (RSV) infections pose a substantial health burden, particularly for clinically vulnerable populations such as infants and older adults. Although novel immunoprophylactic interventions show promise in providing protection, many countries may not have robust surveillance systems to monitor circulating RSV lineages and detect mutations that might reduce the effectiveness of these new interventions. We aimed to assess the diversity and temporal dynamics of circulating RSV lineages in urban populations through amplicon-based sequencing and analysis of wastewater extracts. METHODS: In this prospective observational wastewater-based genomic surveillance study, 32 raw influent 24-h composite samples were collected during the 2022-23 and 2023-24 RSV seasons from both Zurich and Geneva, Switzerland. We applied an RSV subtype-specific amplicon-based sequencing approach to obtain RSV-A and RSV-B sequences from all 64 samples. Mutations relative to reference genomes were identified at positions with read depth above 30. Relative abundances of RSV lineages were estimated from frequencies of lineage-signature mutations, present in greater than 90% of publicly available sequences of that lineage. FINDINGS: Relative abundances of RSV-B (2022-23) and RSV-A (2023-24) lineages were estimated over the two RSV seasons. During the 2022-23 season, the RSV-B B.D.E.1 lineage prevailed in both cities. In the 2023-24 season, multiple RSV-A lineages cocirculated, including A.D.1, A.D.3, A.D.5, and their sub-lineages. Identification and frequency estimation of mutations showed low-frequency, non-synonymous mutations in antigenic sites on the fusion gene of both RSV-A and RSV-B, some of which have not been reported in clinical sequences. The primary outcome was identification and relative abundance of RSV lineages in wastewater samples. INTERPRETATION: These findings show the potential of wastewater-based genomic surveillance to identify and track circulating RSV lineages and clinically relevant mutations. As novel RSV immunoprophylaxis measures are introduced in upcoming RSV seasons, wastewater-derived genomic RSV data provide a valuable baseline for understanding RSV diversity and future viral evolution under increased immunological pressure. FUNDING: This study was funded by the Swiss National Science Foundation and in part by the National Institute Of Allergy And Infectious Diseases of the National Institutes of Health. Funding for sample collection and processing was provided by the Swiss Federal Office of Public Health.
Humans↗
DNA base sequence homologies among strains of Streptococcus sanguis.
DNA was isolated from 19 strains and substrains of Streptococcus sanguis and analysed for guanine plus cytosine (GC) contents and base sequence homologies. Three groups could be discerned: group 1 strains had 40-8 to 42-8 mol % GC; group 2, 42-7 to 44-0 mol % GC; group 3, 43-8 to 46-4 mol % GC. DNA homologies between groups 1 and 3 were 40 to 60% at 67 degrees C and 40% at 72 degrees C. The homologies of group 2 towards groups 1 and 3 were much lower. Strains in groups 1 and 3 hydrolysed arginine and aesculin and fermented inulin; group 2 strains did not. Groups 1 and 3 could be considered subspecies of S. sanguis. Group 2 should not be considered S. sanguis.
Arginine↗
Detection of virus-specific DNA and RNA base-sequences in individual cells transformed or infected by adenovirus type 2.
By means of 3H thymidine-labelled adenovirus 2 DNA, adenovirus-specific DNA sequences have been localized in individual nuclei of adenovirus 2- or 12-infected cells, and adenovirus-specific RNA sequences have been detected in the permissive cells as well as in cells transformed by adenovirus type 2. The ability to detect such specific virus RNA base-sequences in particular, by in situ hybridization, should be useful in studying the transcriptional specificities of tumours and neoplasms.
Adenoviridae↗
A novel representation of the conformational structure of transfer RNAs. Correlation of the folding patterns of the polynucleotide chain with the base sequence and the nucleotide backbone torsions.
A novel description of the conformational characteristics of all the individual nucleotides and the phosphodiesters in tRNAs is presented in the form of a circular plot. This representation furnishes information of the base sequence with the folding patterns of the polynucleotide chain as one traverses along the circumference and with the individual nucleotide and phosphodiester linkage torsions along the radii. The circular plot obtained for yeast tRNAPhe strikingly distinguishes the helical and the loop regions. The variation of the different nucleotide torsions along the entire chain length and their effect on the secondary helical and tertiary loop regions become readily apparent.
Base Sequence↗
Conservation of repeated DNA base sequences in Crustacea: a molecular approach to decapod phylogeny.
Analysis of data obtained from molecular hybridization of 3H-labeled repetitious DNA has been utilized to reconstruct the broad outlines of phylogenetic relationships among decapod Crustacea. This molecular reconstruction agrees reasonably well with the paleontological record, and with other schemes obtained by comparative morphological and serological approaches. Preliminary evidence is in line with the hypothesis that continuous addition of new repeated sequence families to the genome over long periods of time may in part account for the correlation observed between percent repetitious DNA hybridized and divergence time. It is tentatively concluded that a core of DNA base sequence homology has been highly conserved throughout the evolution of the Crustacea. Demonstration of inter-species sequence homology has important implications to models which relegate a genetic regulatory function to repeated DNAs.
Animals↗
DNA base sequence of the po promoter region of phage lamdba.
The sequence of a 123 base pair HpaII restriction fragment of bacteriophage lamdba DNA has been determined by the dimethylsulphate-hydrazine technique. Of this fragment 65 nucleotide pairs are transcribed into the 5' proximal part of the oop RNA. The remaining 58 nucleotide pairs preceding the start point of transcription show homologies to the lamdbaL and lamdbapR promoter regions, and are concluded to contain the lamdbapo promoter sequence.
Base Sequence↗
[A new method for DNA base sequence determination].
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Base Sequence↗