bioRxiv Science⌕ Search

Biology subjects

Bristow, J.

Publications and source records attributed to Bristow, J..

3 recordsLinked to original sources

TEgenomeSimulator: A Flexible Framework for Simulating Genomes with Configurable Transposable Element Landscapes

Transposable elements (TEs) are major contributors to genome structure and evolution. However, our ability to study them is limited by the difficulty of annotating and curating them, especially in non-model organisms. This challenge is compounded by a lack of ground-truth datasets for benchmarking, which are nearly impossible to generate through manual curation alone. To overcome this critical limitation, we developed TEgenomeSimulator, a flexible framework for generating synthetic genomes with configurable TE landscapes. TEgenomeSimulator supports both randomly generated and biologically derived backbone sequences, enabling the modeling of TE insertions under diverse structural and evolutionary contexts. Benchmarking against existing simulators demonstrated that TEgenomeSimulator reproduces realistic TE composition, sequence divergence, and integrity distributions while offering greater flexibility in modeling chromosome-level structure. Its modular design offers a tuneable continuum between biological fidelity and experimental control, facilitating systematic benchmarking, algorithm development, and evolutionary modeling of TE dynamics in silico, filling a major gap in the field. The source code of TEgenomeSimulator and the scripts for this paper are available at https://github.com/Plant-Food-Research-Open/TEgenomeSimulator.

bioinformatics↗

Responses of the putative trachoma vector, Musca sorbens, to volatile semiochemicals from human faeces

BackgroundThe putative vector of trachoma, Musca sorbens, prefers to lay its eggs on human faeces on the ground. This study sought to determine whether M. sorbens females were attracted to volatile odours from human faeces in preference to odours from the faeces of other animals, and to determine whether specific volatile semiochemicals mediate selection of the faeces.\n\nMethodology/Principal findingsTraps baited with the faeces of humans and local domestic animals were used to catch flies at two trachoma-endemic locations in The Gambia and one in Ethiopia. At all locations, traps baited with faeces caught more female M. sorbens than control traps baited with soil, and human faeces was the most successful bait compared with soil (mean rate ratios 44.40, 61.40, 10.50 [P<0.001]; 8.17 for child faeces [P=0.004]). Odours from human faeces and some domestic animals were sampled by air entrainment. Extracts of the volatiles from human faeces were tested by coupled gas chromatography-electroantennography with laboratory-reared female M. sorbens. Twelve compounds were electrophysiologically active and tentatively identified by coupled mass spectrometry-gas chromatography, these included cresol, indole, 2-methylpropanoic acid, butanoic acid, pentanoic acid and hexanoic acid.\n\nConclusions/SignificanceIt is possible that some of these volatiles govern the strong attraction of M. sorbens flies to human faeces. If so, a synthetic blend of these chemicals, at the correct ratios, may prove to be a highly attractive lure. This could be used in odour-baited traps for monitoring or control of this species in trachoma-endemic regions.\n\nAuthor summaryMusca sorbens, also known as the Bazaar Fly, visits peoples faces to feed on ocular and nasal discharge. While feeding, M. sorbens can transmit Chlamydia trachomatis, the bacterium that causes the infectious eye disease trachoma. Around 1.9 million people worldwide are visually impaired or blind from this disease. Although it is believed that M. sorbens transmits trachoma, very few studies have looked at ways to control this fly. A large-scale trial has shown that control of fly populations with insecticide reduces active trachoma disease prevalence. Odour-baited traps for the suppression of disease vector populations are an attractive option as there is no widespread spraying of insecticide, however, highly attractive baits are critical to their success. Here we demonstrate that the preference of these flies for breeding in human faeces is probably mediated by odour cues, and we isolate chemicals in the odour of human faeces that cause a response in the antennae of M. sorbens. These compounds may play a role in the specific attractiveness of human faeces to these flies, perhaps by being present in greater amounts or at favourable ratios. These may be developed into a chemical lure for odour-baited trapping to suppress M. sorbens populations.

ecology↗

Genome-Wide Fetalization of Enhancer Architecture in Heart Disease

Heart disease is associated with re-expression of key transcription factors normally active only during prenatal development of the heart. However, the impact of this reactivation on the genome-wide regulatory landscape in heart disease has remained obscure. Here we show that pervasive epigenomic changes occur in heart disease, with thousands of regulatory sequences reacquiring fetal-like chromatin signatures. We used RNA-seq and ChIP-seq targeting a histone modification associated with active transcriptional enhancers to generate genome-wide enhancer maps from left ventricle tissue from 18 healthy controls and 18 individuals with idiopathic dilated cardiomyopathy (DCM). Healthy individuals had a highly reproducible epigenomic landscape, consisting of more than 31,000 predicted heart enhancers. In contrast, we observed reproducible disease-associated gains or losses of activity at more than 7,500 predicted heart enhancers. Next, we profiled human fetal heart tissue by ChIP-seq and RNA-seq. Comparison with adult tissues revealed that the heart disease epigenome and transcrip-tome both shift toward a fetal-like state, with 3,400 individual enhancers sharing fetal regulatory properties. Our results demonstrate widespread epigenomic changes in DCM, and we provide a comprehensive data resource (http://heart.lbl.gov) for the mechanistic exploration of heart disease etiology.

genomics↗