Base Pair Sequence Research Articles

Panacus: fast and exact pangenome growth and core size estimation.

Using a single linear reference genome poses a limitation to exploring the full genomic diversity of a species. The release of a draft human pangenome underscores the increasing relevance of pangenomics to overcome these limitations. Pangenomes are commonly represented as graphs, which can represent billions of base pairs of sequence. Presently, there is a lack of scalable software able to perform key tasks on pangenomes, such as quantifying universally shared sequence across genomes (the core genome ) and measuring the extent of genomic variability as a function of sample size ( pangenome growth ). We introduce Panacus (pangenome-abacus), a tool designed to rapidly perform these tasks and visualize the results in interactive plots. Panacus can process GFA files, the accepted standard for pangenome graphs, and is able to analyze a human pangenome graph with 110 million nodes in less than one hour. Panacus is implemented in Rust and is published as Open Source software under the MIT license. The source code and documentation are available at https://github.com/marschall-lab/panacus . Panacus can be installed via Bioconda at https://bioconda.github.io/recipes/panacus/README.html . Luca Parmigiani ( luca.parmigiani@uni-bielefeld.de ), Daniel Doerr ( daniel.doerr@hhu.de ).

Multifractal Properties of Human Chromosome Sequences

The intricacy and fractal properties of human DNA sequences are examined in this work. The core of this study is to discern whether complete DNA sequences present distinct complexity and fractal attributes compared with sequences containing exclusively exon regions. In this regard, the entire base pair sequences of DNA are extracted from the NCBI (National Center for Biotechnology Information) database. In order to create a time series representation for the base pair sequence {G,C,T,A}, we use the Chaos Game Representation (CGR) approach and a mapping rule f, which enables us to apply the metric known as the Complexity–Entropy Plane (CEP) and multifractal detrended fluctuation analysis (MF-DFA). To carry out our investigation, we divided human DNA into two groups: the first is composed of the 24 chromosomes, which comprises all the base pairs that form the DNA sequence, and another group that also includes the 24 chromosomes, but the DNA sequences rely only on the exons’ presence. The results show that both sets provide fractal patterns in their structure, as obtained by the CGR approach. Complete DNA sequences show a sharper visual fractal pattern than sequences composed only of exons. Moreover, the sequences occupy distinct areas of the complexity–entropy plane, and the complete DNA sequences lead to greater statistical complexity and lower entropy than the exon sequences. Also, we observed that different fractal parameters between chromosomes indicate diversity in genomic sequences. All these results occur in different scales for all chromosomes.

Multifractal analysis of maize and soybean DNA

This paper investigates the complexity of DNA sequences in maize and soybean using the multifractal detrended fluctuation analysis (MF-DFA) method, chaos game representation (CGR), and the complexity-entropy plane approach. The study aims to understand the patterns and structures of these DNA sequences, which can provide insights into their genetic makeup and improve crop yield and quality. The results show that maize and soybean DNA sequences exhibit fractal properties, indicating a complex and self-organizing structure. We observe the persistence trend between sequences of base pairs, which indicates long-range correlations between base pairs. We also identified the stochastic nature of the DNA sequences of both species.

Mapping of DNA base-pair sequence from breathing dynamics of hetero-polymeric DNA: A genetic algorithm-based study

Mapping of DNA base-pair sequence from breathing dynamics of hetero-polymeric DNA: A genetic algorithm-based study

A novel inducible von Willebrand Factor Cre recombinase mouse strain to study microvascular endothelial cell-specific biological processes in vivo

Mouse models are invaluable to understanding fundamental mechanisms in vascular biology during development, in health and different disease states. Several constitutive or inducible models that selectively knockout or knock in genes in vascular endothelial cells exist; however, functional and phenotypic differences exist between microvascular and macrovascular endothelial cells in different organs. In order to study microvascular endothelial cell-specific biological processes, we developed a Tamoxifen-inducible von Willebrand Factor (vWF) Cre recombinase mouse in the SJL background. The transgene consists of the human vWF promoter with the microvascular endothelial cell-selective 734 base pair sequence to drive Cre recombinase fused to a mutant estrogen ligand-binding domain [ERT2] that requires Tamoxifen for activity (CreERT2) followed by a polyadenylation (polyA) signal. We initially observed Tamoxifen-inducible restricted bone marrow megakaryocyte and sciatic nerve microvascular endothelial cell Cre recombinase expression in offspring of a mixed strain hemizygous C57BL/6-SJL founder mouse bred with mT/mG mice, with >90% bone marrow megakaryocyte expression efficiency. Founder mouse offspring were backcrossed to the SJL background by speed congenics, and intercrossed for >10 generations to develop hemizygous Tamoxifen-inducible vWF Cre recombinase (vWF-iCre/+) SJL mice with stable transgene insertion in chromosome 1. Microvascular endothelial cell-specific Cre recombinase expression occurred in the sciatic nerves, brains, spleens, kidneys and gastrocnemius muscles of adult vWF-iCre/+ SJL mice bred with Ai14 mice, with retained low level bone marrow and splenic megakaryocyte expression. This novel mouse strain would support hypothesis-driven mechanistic studies to decipher the role(s) of specific genes transcribed by microvascular endothelial cells during development, as well as in physiologic and pathophysiologic states in an organ- and time-dependent manner.

Sequence composition changes in short tandem repeats: heterogeneity, detection, mechanisms and clinical implications.

Short tandem repeats (STRs) are a class of repetitive elements, composed of tandem arrays of 1-6 base pair sequence motifs, that comprise a substantial fraction of the human genome. STR expansions can cause a wide range of neurological and neuromuscular conditions, known as repeat expansion disorders, whose age of onset, severity, penetrance and/or clinical phenotype are influenced by the length of the repeats and their sequence composition. The presence of non-canonical motifs, depending on the type, frequency and position within the repeat tract, can alter clinical outcomes by modifying somatic and intergenerational repeat stability, gene expression and mutant transcript-mediated and/or protein-mediated toxicities. Here, we review the diverse structural conformations of repeat expansions, technological advances for the characterization of changes in sequence composition, their clinical correlations and the impact on disease mechanisms.

A NEW SPECIES OF THELOHANELLUS (CNIDARIA: MYXOSPOREA: MYXOBOLIDAE) FROM THE GILL OF QUILLBACK, CARPIODES CYPRINUS (CYPRINIFORMES: CATOSTOMIDAE), FROM THE ARKANSAS RIVER DRAINAGE OF OKLAHOMA.

During May 2022 and again in March 2023, 5 quillbacks, Carpiodes cyprinus, were collected from the Verdigris River, Wagoner County, Oklahoma (n = 1), and the Black River, Lawrence County, Arkansas (n = 4), and their gill, gallbladder, fins, integument, musculature, and other major organs were macroscopically examined for myxozoans. Gill lamellae from the single quillback from the Verdigris River was infected with a new myxozoan, Thelohanellus oklahomaensis n. sp. Qualitative and quantitative morphological data were obtained from fresh and formalin-fixed preserved myxospores, and molecular data consisted of a 1,767 base pair sequence of the partial small subunit (SSU) ribosomal RNA gene. Phylogenetic analysis grouped T. oklahomaensis n. sp. with myxozoans known to infect North American catostomids and Eurasian cyprinids. Histological examination localized plasmodia to an intralamellar developmental site and revealed a possible vestige of a second polar capsule. Although plasmodia markedly expanded lamellae, there were no associated epithelial or inflammatory changes. Thelohanellus oklahomaensis n. sp. is the only member of the genus known to infect the gills of C. cyprinus.

Probing the modulation in facilitated diffusion guided by DNA-protein interactions in target search processes.

Many fundamental biophysical processes involving gene regulation and gene editing rely, at the molecular level, on an intricate methodology of searching and locating the precise target base pair sequence on the genome by specific binding proteins. A unique mechanism, known as 'facilitated diffusion', which is a combination of 1D sliding along with 3D movement, is considered to be the key step for such events. This also explains the relatively much shorter timescale of the target searching process, compared to other diffusion-controlled biophysical processes. In this work, we aim to probe the modulation of target search dynamics of a protein moiety by estimating the rate of the target search process, and the statistics of the search rounds and timescales accomplished by the 1D and 3D motions, based on first passage time (FPT) calculations. This is studied with its characteristics getting influenced by various given conditions such as, when the DNA is rigid or flexible, and when the target is placed at different locations on the DNA. The current theoretical framework includes a Brownian dynamics simulation setup adopting a straightforward coarse-grained model for a diffusing protein on DNA. Moreover, this theoretical analysis provides insights into the complex target search dynamics by highlighting the significance of the chain dynamics in the mechanistic details of the facilitated diffusion process.

DNA Barcoding of Anchovy in Tuban Regency as Database of Indonesian Marine Genetic Diversity

Anchovy is the main catch and the primary consumption of coastal communities in Indonesia, and its production shows an increase of more than 10% in 2021. Tuban district, in East Java, Indonesia is part of the WPP 712 (Wilayah Pengelolaan Perikanan or Fisheries Management Area) and highly produces anchovies’ fisheries. Anchovy has a small size, making it difficult to identify morphologically. This study aimed to genetically identify anchovy samples obtained from North Java (Tuban) waters. Molecular identification was conducted by utilizing Cytochrome Oxidase Subunit I (COI) gene using jg-HCO and jg-LCO primers. This study observed 12 individual samples with 623 base pair sequence length. Five species were obtained, namely four species of anchovies (Encrasicholina heteroloba, Encrasicholina punctifer, Stolephorus waitei, and Stolephorus insularis) and one species of sardines (Dussumieria elopsoides) with 99.84-100% similarity to NCBI sequences data. Anchovies typically have a streamlined body with a slightly compressed shape. Anchovies have cycloid scales, which are smooth-edged and relatively small, ranging from a few centimeters to around 20 centimeters in length. Some of the genus from the Anchovy group are Encrasicholina and Stolephorus. The phylogenetic tree reconstruction leads into four clades with a genetic distance between clades of 17,9-24,5 %. This research provides methods and data on the genetic diversity of anchovies taxa caught in Tuban, East Java. The findings are expected to support promoting new standards for healthier and more sustainable anchovy stocks in the country. Overall, this study contributes to providing valuable insights for fisheries management and conservation efforts in Indonesia.

69 The Bigger Picture of Phenomics: Whole-System Support for Systems Research, Models and Databases

Abstract Phenomics started with Mendel’s elegantly simple empirical studies. Soon after, Fisher discovered purines were rich in nuclei of all cells. A century later, we have the technology to compare the actual base pair sequence of DNA and RNA with the outward expressions of phenotypes. We have sire evaluation based on genomic and phenomic measure. But, being human, it is quite common to get immersed in exciting technology and tend to forget why we developed the technology in the first place. We only refer to ensuring a stable efficient food supply of plants and animals in the reports that we expect decision makers to read and give us more money. It is, however, truly wonderful that we now have the techniques to study the questions of the ages. But the future of phenomics is built on the foundations of the past. In 1974, A. E. Freeman and others convened a meeting under the mechanism of the newly formed Regional Research Project 2 on Defining the Inefficiency of Animal Production. From that workshop came the first modern multistate genetic study in dairy cattle with the objective to compare the phenotypes (milk component production, energy and nitrogen metabolism, hormones) of dairy animals that were born from bulls of High (+795 kg PTAM) and Low (167 kg PTAM) bulls. Please remember this study was designed in the mid 1970s and the first data collected in the early 1980s, decades before efficient methods of DNA and RNA composition were available. Studies conducted at Washington State University demonstrated marked genetic and environmental differences in adipose tissues of dairy animals. Enzymes involved with catabolic reactions were highly associated with High PTAM bulls while enzymes associated with anabolic reactions in adipose tissue were more closely related to increased energy intake regardless of genetic background. With mRNA chips, we were able, after almost 40 years, to directly relate variation in mRNA expression in the adipose tissue with the genetic background of the animals. This was the first such discovery in the field, and has led to more defined and expansive phenomics studies. In the year 2023, the use of genomics, phenomics, databases, large scale, cooperative studies and team science are specific recommendations, strategies and goals of the USDA, NIFA, The National Academies, and Land-Grant Universities. The AgBioData consortium is one example of international teams working together to expand the use of genetic and genomic databases, to prepare undergraduate and graduate level educational materials on FAIR databases and to encourage and support sustainable, robustly funded public and private partnerships in the use of integrated studies and large databases, including phenomics, with the sole purpose of expanding a robust, resilient, safe and plentiful food supply.

Two different types of tandem sequences mediate the overexpression of TinCYP51B in azole-resistant Trichophyton indotineae.

Trichophyton indotineae is an emerging dermatophyte that causes severe tinea corporis and tinea cruris. Numerous cases of terbinafine- and azole-recalcitrant T. indotineae-related dermatophytosis have been observed in India over the past decade, and cases are now being recorded worldwide. Whole genome sequencing of three azole-resistant strains revealed a variable number of repeats of a 2,404 base pair (bp) sequence encoding TinCYP51B in tandem specifically at the CYP51B locus position. However, many other resistant strains (itraconazole MIC ≥0.25 µg/mL; voriconazole MIC ≥0.25 µg/mL) did not contain such duplications. Whole-genome sequencing of three of these strains revealed a variable number of 7,374 bp tandem repeat blocks harboring TinCYP51B. Consequently, two types of T. indotineae azole-resistant strains were found to host TinCYP51B in tandem sequences (type I with 2,404 bp TinCYP51B blocks and type II with 7,374 bp TinCYP51B blocks). Using the CRISPR/Cas9 genome-editing tool, the copy number of TinCYP51B within the genome of types I and II strains was brought back to a single copy. The azole susceptibility of these modified strains was similar to that of strains without TinCYP51B duplication, showing that azole resistance in T. indotineae strains is mediated by one of two types of TinCYP51B amplification. Type II strains were prevalent among 32 resistant strains analyzed using a rapid and reliable PCR test.

Effect of Carcinomas on Autosomal Trait Screening: A Review Article.

This review highlights the effect of carcinomas on the results of the examination of autosomal genetic traits for identification and paternity tests when carcinoid tissue is the only source and no other samples are available. In DNA typing or genetic fingerprinting, variable elements are isolated and identified within the base pair sequences that form the DNA. The person's probable identity can be determined by analysing nucleotide sequences in particular regions of DNA unique to everyone. Genetics plays an increasingly important role in the risk stratification and management of carcinoma patients. The available information from previous studies has indicated that in some incidents, including mass disasters and crimes such as terrorist incidents, biological evidence may not be available at the scene of the accident, except for some unknown human remains found in the form of undefined human tissues. If these tissues have cancerous tumours, it may affect the examination of the genetic traits derived from these samples, thereby resulting in a failure to identify the person. Pathology units, more often, verify the identity of the patients who were diagnosed with cancer in reference to their deceased tumorous relatives. Genetic fingerprinting (GF) is also used in paternity testing when the alleged parent disappeared or died and earlier was diagnosed and treated for cancer.

New Record: Molecular Depiction of Rhamnolipids (rhlA) Gene in Locally Isolated Strains of Pseudomonas aeruginosa

Soil samples were collected from oil-contaminated sites which were located in west Qurna, Basrah, Iraq. Pseudomonas species were initially isolated on mineral salts and Pseudomonas agar media and identified using morphological and biochemical characterizations. Then, specific primers for the rhlA gene belonging to Pseudomonas aeruginosa were designed based on the primer design conditions, and PCR was performed to amplify the 888 bp size fragment of the rhlA gene; additionally, the primary PCR products were purified and sent for sequencing. The band of about 888bp was determined on the gel, the amplified rhlA gene sequencing findings were revised, only 366 bp were ready to analyze using the (BLAST) software, and the final result was identified as a partial sequence of chromosomal rhlA gene related to Pseudomonas aeruginosa with percent identity of 99.45%. The query gene’s incomplete matching with another partial rhlA record on NCBI was caused by variations in two base pair sequences (T in sequence 348 and C in sequence 353, respectively), and despite the small difference, this results in variation in the amino acids produced; so that a new record number, ON637169, was assigned when the sequence was deposited in GenBank. The relation among the new record of partial rhlA gene with the same number of the other rhlA gene sequences (60 records) was demonstrated by creating a phylogenetic tree.

Base pair compositional variability influences DNA structural stability and tunes hydration thermodynamics and dynamics.

DNA deformability and differential hydration are crucial determinants of biological processes ranging from genetic material packaging to gene expression; their associative details, however, remain inadequately understood. Herein, we report investigations of the dynamic and thermodynamic responses of the local hydration of a variety of base pair sequences. Leveraging in silico sampling and our in-house analyses, we first report the local conformational propensity of sequences that are either predisposed toward the canonical A- or B-conformations or are restrained to potential transitory pathways. It is observed that the transition from the unrestrained A-form to the B-form leads to lengthwise structural deformation. The insertion of intermittent -(CG)- base pairs in otherwise homogeneous -(AT)- sequences bears dynamical consequences for the vicinal hydration layer. Calculation of the excess (pair) entropy suggests substantially higher values of hydration water surrounding A conformations over the B- conformations. Applying the Rosenfeld approximation, we project that the diffusivity of water molecules proximal to canonical B conformation is least for the minor groove of the canonical B-conformation. We determine that structure, composition, and conformation specific groove dimension together influence the local hydration characteristics and, therefore, are expected to be important determinants of biological processes.

The complete sequence of a human Y chromosome.

The human Y chromosome has been notoriously difficult to sequence and assemble because of its complex repeat structure that includes long palindromes, tandem repeats and segmental duplications1-3. As a result, more than half of the Y chromosome is missing from the GRCh38 reference sequence and it remains the last human chromosome to be finished4,5. Here, the Telomere-to-Telomere (T2T) consortium presents the complete 62,460,029-base-pair sequence of a human Y chromosome from the HG002 genome (T2T-Y) that corrects multiple errors in GRCh38-Y and adds over 30 million base pairs of sequence to the reference, showing the complete ampliconic structures of gene families TSPY, DAZ and RBMY; 41 additional protein-coding genes, mostly from the TSPY family; and an alternating pattern of human satellite 1 and 3 blocks in the heterochromatic Yq12 region. We have combined T2T-Y with a previous assembly of the CHM13 genome4 and mapped available population variation, clinical variants and functional genomics data to produce a complete and comprehensive reference sequence for all 24 human chromosomes.

Causes of DNA Damage and Genomic Instability: A Review

Genomic instability defines all genetic alterations resulting from excessive or high frequency of mutation; base pairs sequence alterations known as microsatellite instability (MSI) and aneuploidy also called chromosome instability (CIN), chromosomal re- arrangements within the genome or the susceptibility of genome to alterations that occur during cell division cycle. The genome of most cancer cells is highly unstable, mostly due to damage to tumour suppressor genes example tp53 which encodes p53 or other genes coordinating cell division. Telomere is a nucleoprotein complex which extends the physical ends of eukaryotic chromosomes, protecting it from degradation, counteracting sequence loss, protecting genes closer to the chromosomes end and inhibiting cell cycle arrest. Studies have implicated the dysfunction of telomere to the formation of sub-tetraploid aneuploid cells that exhibit tumourigenic capacity and formation of anueploid cells that can elude programmed cell death (apoptosis) and form tumour cells, thus initiating genomic instability. In this review, we presented an insight to the causes of DNA damage and its associated genomic instability. We found that many factors such as fragile sites, end replication problem, DNA double strand breaks, DNA replication defects, deletion, insertion and translocation all are responsible to the fragile nature of the genome.

Abstract P1008: Characterizing Complex Tandem Repeat Variants And Their Contribution To Congenital Heart Disease

Congenital heart disease (CHD) is a major cause of childhood mortality and lifelong morbidity in children and adults. CHD has a strong genetic basis, with exome and short read whole genome sequencing (srWGS) identifying genetic contributions to CHD risk in around 45% of affected individuals, while the remaining 55% have not had a specific genetic risk identified. Variation in tandem repeats (TRs), defined as repeated sequences of base pairs, has been implicated in several diseases and can affect gene expression. TR polymorphism in coding or regulatory regions of CHD related genes can alter function and expression, thereby modifying risk of CHD in patients. Identifying variants in TRs has been a challenge due to multiple variants at each site, as well as difficulty resolving long expansions with short read sequencing technologies. New bioinformatic tools have enabled identification of high-confidence short-TR (STR) variants in srWGS. Additionally, long read whole genome sequencing (lrWGS), with read lengths of 10-20 kilobases, enables genotyping of longer TRs that are missed by srWGS. We hypothesized that patients with CHD will have a higher burden of de novo and transmitted TRs near known CHD genes. We identified de novo and transmitted STR variants near known CHD genes in srWGS data from 1900 CHD proband and their parents in the Pediatric Cardiac Genomics Consortium (PCGC), and 1611 non-CHD probands and their parents. Transmitted STR variants in CHD probands were enriched in 5’-UTR, introns, and promoters of CHD genes compared to non-CHD probands. We identified large de novo repeats near known CHD genes such as NOTCH2 and RBFOX2 . Additionally we used Pacbio HiFi lrWGS on 150 PCGC probands without an established etiology for CHD. Combining these analyses, we identified 3,243 repeat regions with low read depth in srWGS, and therefore unable to be resolved accurately, near known CHD genes and from lrWGS we assess length polymorphisms using Tandem Repeat Finder. TRs that harbor large variation in length were identified within intronic regions of CHD genes including FLT4 , NFATC1 , and PKD1 . We suggest that polymorphic repeat regions provide new candidate variants or altering gene transcription or splicing and thereby contribute to CHD.

The emergence of precision medicine for oncology

The emergence of precision medicine for oncology Dr Priya Hays, PhD, considers how the rapid development of precision medicine for oncology has impacted diagnosis, treatment, and clinical outcomes in cancer care. Personalised medicine, also referred to as precision medicine, had its early conceptual foundations in the Human Genome Project, the multi-institutional effort to sequence the entire base pair sequences of the human genome, or DNA sequences in the cell. The sequencing revealed variations between individuals in their DNA sequences. This variation, or what came to be known as genomic variation, could be mobilised to differentiate diagnosis and treatment between individual genomes. Targeted therapies - small molecule inhibitors designed to attack cancer cells exclusively by affecting signalling pathways - were developed as viable treatment options defined by the personalised medicine pathway.

The role of transcript regions and amino acid choice in nucleosome positioning.

Eukaryotic DNA is organized and compacted in a string of nucleosomes, DNA-wrapped protein cylinders. The positions of nucleosomes along DNA are not random but show well-known base pair sequence preferences that result from the sequence-dependent elastic and geometric properties of the DNA double helix. Here, we focus on DNA around transcription start sites, which are known to typically attract nucleosomes in multicellular life forms through their high GC content. We aim to understand how these GC signals, as observed in genome-wide averages, are produced and encoded through different genomic regions (mainly 5' UTRs, coding exons, and introns). Our study uses a bioinformatics approach to decompose the genome-wide GC signal into between-region and within-region signals. We find large differences in GC signal contributions between vertebrates and plants and, remarkably, even between closely related species. Introns contribute most to the GC signal in vertebrates, while in plants the exons dominate. Further, we find signal strengths stronger on DNA than on mRNA, suggesting a biological function of GC signals along the DNA itself, as is the case for nucleosome positioning. Finally, we make the surprising discovery that both the choice of synonymous codons and amino acids contribute to the nucleosome positioning signal.

Diagnosis and Treatment of Gordonia Species Infection in a Peach-Faced Lovebird (Agapornis roseicollis).

Respiratory distress is a common presentation for avian species. A 9-week-old peach-faced lovebird (Agapornis roseicollis) was presented with a 2-week history of progressive dyspnea. Computed tomographic (CT) images were suggestive of splenomegaly and bilateral granulomatous pulmonary disease. Polymerase chain reaction testing of samples from the choana, cloaca, and distal tracheal/syringeal area were positive for Mycobacterium species hsp65. A comparison search of the 400 base pair sequence in the NCBI/BLAST/blastn database revealed a best match of 93% similarity to Gordonia species and 91% similarity to Gordonia bronchialis. Gordonia is a genus in the phylum Actinomycetota, the same lineage that includes Mycobacterium species. Gordonia species can be mistaken for Mycobacterium species unless more definitive diagnostic testing is pursued. Infection caused by Gordonia species is rare in humans. Reports commonly cite infection of immunocompromised patients, and to our knowledge, no reports of treatment have been published in the veterinary literature. After the test results were obtained, the patient was treated with azithromycin and pradofloxacin for 3 months. The lovebird was presented for reexamination when the antibiotic treatment was complete. When reexamined, and a second series of CT images evaluated, it was determined that the treatment achieved clinical resolution of signs and lesions.