Related papers: Units of genetic transfer in prokaryotes

The GC content of prokaryotic genomes is species-specific and takes values from 16 to 77 percent. There are currently no accepted explanations for this diversity of selection for GC content. We analyzed the known correlations between GC…

Horizontal gene Transfer (HT) denotes the transmission of genetic material between two living organisms, while the vertical transmission refers to a DNA transfer from parents to their offspring. Consistent experimental evidence report that…

Horizontal gene transfer (HGT) is an important process in bacterial evolution. Current phylogeny-based approaches to capture it cannot however appropriately account for the fact that HGT can occur between bacteria living in different…

Phylogenetic trees illustrate the evolutionary history of genes and species. In most cases, although genes evolve along with the species they belong to, a species tree and gene tree are not identical, because of evolutionary events at the…

By means of the concept of factorial moment the charge transfer rates in DNA segments with fractal structures are investigated. An analytical form for the electron transfer rate is obtained.

Charge transfer is considered in systems composed of a donor, an acceptor and bridge sites of (AT) nucleotide pairs. For a bridge consisting of 180 (AT) pairs, three cases are dealt with: a uniform case, when all the nucleotides in each…

The original problem of phyllotaxis was focused on the regular arrangements of leaves on mature stems represented by common fractions such as 1/2, 1/3, 2/5, 3/8, 5/13, etc. The phyllotaxis fraction is not fixed for each plant but it may…

The time required to transcribe genes with long primary transcripts may limit their ability to be expressed in cells with short mitotic cycles, a phenomenon termed intron delay. As such short cycles are a hallmark of the earliest stages of…

This groundbreaking study explores the expanse of Large Language Models (LLMs), such as Generative Pre-Trained Transformer (GPT) and Bidirectional Encoder Representations from Transformers (BERT) across varied domains ranging from…

Motivation: LTR retrotransposons are mobile elements that are able, like retroviruses, to copy and move inside eukaryotic genomes. In the present work, we propose a branching model for studying the propagation of LTR retrotransposons in…

Genomes in living organisms consist of the nucleotides adenine (A), guanine (G), cytosine (C) and thymine (T). All prokaryotes have genomes consisting of double-stranded DNA, where the A's and G's (purines) of one strand bind respectively…

Distributions of triplets in some genetic sequences are examined and found to be well described by a 2-parameter Markov process with a sparse transition matrix. The variances of all the relevant parameters are not large, indicating that…

It has been reported that the number of transcription factors encoded in prokaryotic genomes scales approximately quadratically with their total number of genes. We propose a conceptual explanation of this finding and illustrate it using a…

Unit tests play a vital role in uncovering potential faults in software. While tools like EvoSuite focus on maximizing code coverage, recent advances in large language models (LLMs) have shifted attention toward LLM-based test generation.…

Across all kingdoms of biological life, protein-coding genes exhibit unequal usage of synonmous codons. Although alternative theories abound, translational selection has been accepted as an important mechanism that shapes the patterns of…

Few-shot crosslingual transfer has been shown to outperform its zero-shot counterpart with pretrained encoders like multilingual BERT. Despite its growing popularity, little to no attention has been paid to standardizing and analyzing the…

We describe the distribution of Guanine and Cytosine (GC) content in the third codon position (GC3) distributions in different species, analyze evolutionary trends and discuss differences between genes and organisms with distinct GC3…

Nonlinear superlattices exhibit unique features allowing for wave manipulations. Despite the increasing attention received, the underlying physical mechanisms and the evolution process of the band structures and bandgaps in strongly…

Plant phenotyping (Guo et al. 2021; Pieruschka et al. 2019) focuses on studying the diverse traits of plants related to the plants' growth. To be more specific, by accurately measuring the plant's anatomical, ontogenetical, physiological…

We have analyzed DNA sequences of known genes from 16 yeast chromosomes (Saccharomyces cerevisiae) in terms of oligonucleotides. We have noticed that the relative abundances of oligonucleotide usage in the genome follow a long-tail…