Development and functional evaluation of a psoralen-conjugated nucleoside mimic for triplex-forming oligonucleotides by Yu Mikame, Haruki Toyama, Chikara Dohno, Takehiko Wada, Asako Yamayoshi

“…Here, we propose a design of the Ps-TFO for stable triplex formation with target DNA sequences containing pyrimidine-base interruptions under physiological conditions. …”
Get full text

Mutations to transcription factor MAX allosterically increase DNA selectivity by altering folding and binding pathways by Renee Hastings, Arjun K. Aditham, Nicole DelRosso, Peter H. Suzuki, Polly M. Fordyce

“…Towards this end, we study how variants of the promiscuous transcription factor (TF) MAX (H. sapiens) alter DNA specificity and selectivity, yielding >1700 K ds and >500 rate constants in complex with multiple DNA sequences. Twenty-two of the 240 assayed MAX point mutations enhance selectivity, yet none of these mutations occur at residues that contact nucleotides in published structures. …”
Get full text

Representative Metagenomes of Mesophilic Biogas Reactor Across South Korea by Darsha Prabhaharan, Young Wook Go, Hyunjin Kim, Seongcheol Kang, Byoung-In Sang

“…From 110 GB of raw DNA sequences, 401 metagenome-assembled genomes (MAGs) were created, which include 42,301 annotated genes. …”
Get full text

Evaluation of the genome in bird breeding by A. F. Yakovlev, N. V. Dement’eva

“…New technologies determining the DNA sequence of nucleotides have led to the discovery of hundreds of thousands of mononucleotide polymorphic markers, some of which are associated with breeding quality of animals. …”
Get full text

General encoding of canonical k-mers by Wittler, Roland

“…., when the reading direction of a DNA-sequence is ambiguous, canonical k-mers are considered, i.e., the lexicographically smaller of a given k-mer and its reverse (or reverse complement) is chosen as a representative. …”
Get full text

Handgrip-Ring Structure Sensing Probe Assisted Multiple Signal Amplification Strategy for Sensitive and Label-Free Single-Stranded Nucleic Acid Analysis by Ying Ren, Yu He, Ping Li

“…By utilizing this innovative design, the current biosensor demonstrates a remarkable ability to detect miRNA with a limit as low as 376 aM and single-stranded DNA sequences with a limit as low as 45.3 aM. In addition, it possesses exceptional discrimination capabilities. …”
Get full text

Additions to the Mycosphaerella complex by P.W. Crous, K. Tanaka, B.A. Summerel, J.Z. Groenewald

“…Species in the present study were compared based on their morphology, growth characteristics in culture, and DNA sequences of the nuclear ribosomal RNA gene operon (including ITS1, ITS2, 5.8S nrDNA and the first 900 bp of the 28S nrDNA) for all species and partial actin and translation elongation factor 1-alpha gene sequences for Cladosporium species. …”
Get full text

Epigenetic regulation in coronary artery disease: from mechanisms to emerging therapies by Rui Gao, Rui Gao, Rui Gao, Meilin Liu, Meilin Liu, Meilin Liu, Haoyi Yang, Haoyi Yang, Haoyi Yang, Yuhan Shen, Yuhan Shen, Yuhan Shen, Ni Xia, Ni Xia, Ni Xia

“…Epigenetics is a field investigating heritable alterations in gene expression without DNA sequence changes, such as DNA methylation, histone modifications, and non-coding RNAs. …”
Get full text

A new species of parrot snake, Leptophis (Serpentes: Colubridae) from the Brazilian Cerrado by Nelson R. Albuquerque, Roullien H. Martins, Priscila S. Carvalho, Donald B. Shepard, Diego J. Santana

“…Phylogenetic analysis of 16S mtDNA sequences indicate the new species is the sister taxon of L. dibernardoi, a species occurring in the neighboring Caatinga ecoregion.…”
Get full text

Effective in vivo binding energy landscape illustrates kinetic stability of RBPJ-DNA binding by Duyen Huynh, Philipp Hoffmeister, Tobias Friedrich, Kefan Zhang, Marek Bartkuhn, Francesca Ferrante, Benedetto Daniele Giaimo, Rhett A. Kovall, Tilman Borggrefe, Franz Oswald, J. Christof M. Gebhardt

“…Abstract Transcription factors (TFs) such as RBPJ in Notch signaling bind to specific DNA sequences to regulate transcription. How TF-DNA binding kinetics and cofactor interactions modulate gene regulation is mostly unknown. …”
Get full text

Feline Papillomatosis by Herman Egberink, Katrin Hartmann, Ralf Mueller, Maria Grazia Pennisi, Sándor Belák, Séverine Tasker, Karin Möstl, Diane D. Addie, Corine Boucraut-Baralon, Tadeusz Frymus, Regina Hofmann-Lehmann, Fulvio Marsilio, Etienne Thiry, Uwe Truyen, Margaret J. Hosie

“…Besides cat-specific PVs, DNA sequences most closely related to human and bovine PVs have been detected in feline skin lesions. …”
Get full text

Remodeling Intestinal Flora with Sleeve Gastrectomy in Diabetic Rats by Xiaofei Huang, Pan Weng, Huixin Zhang, Yingli Lu

“…The composition changes of intestinal flora were detected by 16S rDNA sequence analysis. Results. In diabetic rats, weight and fasting blood glucose decreased significantly after sleeve gastrectomy. …”
Get full text

Investigating mobile element variations by statistical genetics by Shohei Kojima

“…Mobile elements are DNA sequences that insert themselves into various genome locations. …”
Get full text

Why morphology matters: the negative consequences of hasty descriptions of putative novelties in asexual ascomycetes by Ondřej Koukol, Gregorio Delgado

“…Descriptions of new fungal species have been almost routinely based on phenotypic studies coupled with single or multigene phylogenetic analyses of DNA sequence data. However, high accessibility of sequencing services together with an increasing amount of available molecular data are providing easier and less critical support for taxonomic novelties without carefully studying the phenotype, particularly morphology. …”
Get full text

Molecular Markers for the Phylogenetic Reconstruction of <i>Trypanosoma cruzi</i>: A Quantitative Review by David Ramírez-Delgado, Carlos Alberto Flores-López

“…Based on three quantitative criteria (the number of phylogenetic informative characters, number of available reference sequences in public repositories, and accessibility to DNA sequences for their use as outgroup sequences), we examine and discuss the most appropriate genetic loci for the genetic typification of <i>T. cruzi</i>. …”
Get full text

Mechanism of Gene Amplification via Yeast Autonomously Replicating Sequences by Shelly Sehgal, Sanjana Kaul, M. K. Dhar

“…The amplification promoting sequences were chosen from the Saccharomyces cerevisiae ARS, 5S rRNA regions of Plantago ovata and P. lagopus, proposed sites of replication pausing at Ste20 gene locus of S. cerevisiae, and the bend DNA sequences within fragile site FRA11A in humans. The gene amplification assays showed that plasmid bearing APS from yeast and human beings led to enhanced protein concentration as compared to the wild type. …”
Get full text

New tribe-level classification of Hypostominae (Loricariidae) based on optimization of morphological states on DNA-based relationships, with descriptions of three new tribes and tw... by Jonathan W. Armbruster, Nathan K. Lujan

“…We re-optimized morphological character-state change by mapping states previously used to infer evolutionary history onto a composite phylogenetic tree inferred from DNA-sequence data. This revealed the strong influence on morphology-based phylogenies of a correlated suite of opercular character states related to the mechanism for cheek odontode eversion. …”
Get full text

Linking Epigenetics to Human Disease and Rett Syndrome: The Emerging Novel and Challenging Concepts in MeCP2 Research by Robby Mathew Zachariah, Mojgan Rastegar

“…Epigenetics refer to inheritable changes beyond DNA sequence that control cell identity and morphology. …”
Get full text

The role of chromatin state in intron retention: A case study in leveraging large scale deep learning models. by Ahmed Daoud, Asa Ben-Hur

“…Large scale genomics deep learning models come in two flavors: the first are large language models of DNA sequences trained in a self-supervised fashion, similar to the corresponding natural language models; the second are supervised learning models that leverage large scale genomics datasets from ENCODE and other sources. …”
Get full text

Cellular Reprogramming, Genome Editing, and Alternative CRISPR Cas9 Technologies for Precise Gene Therapy of Duchenne Muscular Dystrophy by Peter Gee, Huaigeng Xu, Akitsu Hotta

“…In the past decade, the development of two innovative technologies, namely, induced pluripotent stem cells (iPSCs) and the CRISPR Cas9 system, has enabled researchers to model diseases derived from patient cells and precisely edit DNA sequences of interest, respectively. In particular, Duchenne muscular dystrophy (DMD) has been an exemplary monogenic disease model for combining these technologies to demonstrate that genome editing can correct genetic mutations in DMD patient-derived iPSCs. …”
Get full text