Biology subjects

Brand, C.

Publications and source records attributed to Brand, C..

6 recordsLinked to original sources

bioRxiv2026

Targeted Chromosomal Sequencing of Wild Bonobos Identifies a Genetically Distinct Subpopulation East of the Lomami River

Bonobos (Pan paniscus), an endangered species, have for decades been genetically understudied, partly due to difficulties in obtaining high-quality samples. The study of their genome is important not only for understanding their evolution, but also for improving conservation efforts, including population management, diversity and inbreeding assessment, and tracking rescued individuals to combat illegal wildlife trafficking. Here, we use chromosome 21 target capture data from 156 non-invasively collected faecal samples from wild bonobos to perform a comprehensive analysis of their population structure. We confirm the existence of three previously suggested subpopulations identified here as Western, Central and Eastern bonobos which are defined by natural barriers of gene flow such as the Lomami River. By estimating levels of inbreeding, diversity and differentiation, we find support for isolation of mainly Western and Eastern populations and add information on the dispersal routes of their ancestors. We infer split times and separation of these populations and apply a genetic framework to geolocalize samples of unknown origin, showing that locations of their potential origin can be estimated with a precision of up to a median of [~]50 km. Our study provides valuable insight into the evolution and population structure of bonobos and reveals how rivers act as strong barriers between populations. It also offers resources for conservation efforts and highlights the need to monitor bonobo populations more closely, in particular isolated ones. ImpactBonobos have been difficult to study genetically due to their remote forest habitat and endangered status. Here we used non-invasive sampling and chromosome 21 target capture sequencing to perform the most detailed analysis to date of their population structure. We find three main subpopulations and genetic differentiation influenced by river barriers, especially with populations found on the Eastern side of the Lomami river. This data will be useful for identifying the geographic origin of confiscated samples and thus aid bonobo conservation efforts.

bioinformatics↗

bioRxiv2025

Ciprofloxacin resistance in Klebsiella pneumoniae: phenotype prediction from genotype and global distribution of resistance determinants

BACKGROUNDCiprofloxacin resistant Klebsiella pneumoniae is common or emerging in many geographies, and knowledge of local resistance rates is important for empirical therapy. Whilst there are known K. pneumoniae ciprofloxacin resistance determinants, there is a lack of systematic data on the effect of determinants, alone and in combination, and there are no publicly accessible tools for predicting resistance from whole genome sequence data. METHODSThe KlebNET-GSP AMR Genotype-Phenotype Group aggregated a matched genotype-phenotype dataset of n=12,167 K. pneumoniae species complex (KpSC) isolates from 27 countries between 2001-2021. We developed a rules-based classifier to predict ciprofloxacin resistance by categorizing the number of quinolone resistance determining regions mutations in gyrA and parC, the number of plasmid-mediated quinolone resistance genes, and the presence/absence of aac(6')-Ib-cr (which can acetylate ciprofloxacin). Predictive performance was assessed using the discovery dataset, for which we re-phenotyped discrepant isolates; and validated using externally contributed datasets (n=7,030 KpSC isolates). RESULTSThe rules-based classifier predicted R vs S/I with categorical agreement, sensitivity, and specificity >96%, and major/very major error rates <4%. Performance was similar across diverse KpSC sources (human, animal, other), species, and intra-species lineages. External validation of the classifier yielded overall 93.12% categorical agreement [95% confidence interval (CI), 92.50-93.74%], 8.65% major errors [95% CI, 7.34-9.97%], and 6.20% very major errors [95% CI, 5.51-6.90%]. We implemented the classifier in Kleborate, a command-line tool that is integrated into the Pathogenwatch web platform. Using this to assess the global distribution of ciprofloxacin resistance determinants in KpSC genomes available in Pathogenwatch (n=31,319, from 109 countries between years 2000-2023), we observed a significant positive association between national quinolone consumption rates and predicted ciprofloxacin resistance (R2=0.20, p=0.004). CONCLUSIONS Ciprofloxacin resistance phenotypes can be reasonably predicted from genotypes, which is sufficient for informing surveillance. However, unexplained resistance remains and accuracy is insufficient for clinical applications. We demonstrate the value of aggregating genotype-phenotype data to explore resistance mechanisms and develop predictors, but highlight complexities in combining phenotype data from different assays and standards.

genomics↗

bioRxiv2023

G-quadruplexe as a structural modulator of Intron Retention upon viral infection

Amongst the wide array of alternative splicing events (ASE), the intrinsic mechanisms of intron retention have remained elusive. This particular type of ASE has long been characterized as an artifact, but recent studies have shown its implication in numerous diseases. It has also been revealed that numerous viruses choose to disrupt alternative splicing to escape cellular immune response and further their proliferation. The main focus of this study was to investigate the G-quadruplex role in Alternative Splicing Events (ASEs) that occur following Flavivirus infections. After having demonstrated that G-quadruplexes structures are mainly formed in Intron Retained Transcripts by RNA-seq, our attention turned toward the ULK3 gene, coding for a serine/threonine kinase regulating autophagy, an essential mechanism in the cellular response to stress and even pathogen infections. In this study, we revealed the presence of a G-quadruplex in the first intron of the ULK3 gene near the 3 splice site. Furthermore, we assayed the formation and stability of this G-quadruplex in vitro and showed that its formation affects IR, as demonstrated by comparisons between wild-type and mutant transfected mini-genes. Finally, we identified the specific RNA-binding protein signature for this G-quadruplex, thereby uncovering the novel role of G-quadruplexes in Alternative Splicing.

biochemistry↗

bioRxiv2021

Epistatic selection on a selfish Segregation Distorter supergene: drive, recombination, and genetic load

Meiotic drive supergenes are complexes of alleles at linked loci that together subvert Mendelian segregation to gain preferential transmission. In males, the most common mechanism of drive involves the disruption of sperm bearing alternative alleles. While at least two loci are important for male drive-- the driver and the target-- linked modifiers can enhance drive, creating selection pressure to suppress recombination. In this work, we investigate the evolution and genomic consequences of an autosomal multilocus, male meiotic drive system, Segregation Distorter (SD) in the fruit fly, Drosophila melanogaster. In African populations, the predominant SD chromosome variant, SD-Mal, is characterized by two overlapping, paracentric inversion on chromosome arm 2R and nearly perfect (~100%) transmission. We study the SD-Mal system in detail, exploring its components, chromosomal structure, and evolutionary history. Our findings reveal a recent chromosome-scale selective sweep mediated by strong epistatic selection for haplotypes carrying Sd, the main driving allele, and one or more factors within the double inversion. While most SD-Mal chromosomes are homozygous lethal, SD-Mal haplotypes can recombine with other, complementing haplotypes via crossing over and with wildtype chromosomes only via gene conversion. SD-Mal chromosomes have nevertheless accumulated lethal mutations, excess non-synonymous mutations, and excess transposable element insertions. Therefore, SD-Mal haplotypes evolve as a small, semi-isolated subpopulation with a history of strong selection. These results may explain the evolutionary turnover of SD haplotypes in different populations around the world and have implications for supergene evolution broadly.

evolutionary biology↗

bioRxiv2021

Effect of chronic JUUL aerosol inhalation on inflammatory states of the brain, lung, heart and colon in mice

While health effects of conventional tobacco are well defined, data on vaping devices, including the most popular e-cigarette JUUL, are less established. Prior acute e-cigarette studies demonstrated inflammatory and cardiopulmonary physiology changes while chronic studies demonstrated extra-pulmonary effects, including neurotransmitter alterations in reward pathways. In this study we investigated effects of chronic flavored JUUL aerosol inhalation on inflammatory markers in brain, lung, heart, and colon. JUUL induced upregulation of cytokine and chemokine gene expression and increased HMGB1 and RAGE in the nucleus accumbens. Inflammatory gene expression increased in colon, and cardiopulmonary inflammatory responses to acute lung injury with lipopolysaccharide were exacerbated in the heart. Flavor-dependent changes in several responses were also observed. Our findings raise concerns regarding long-term risks of e-cigarette use as neuroinflammation may contribute to behavioral changes and mood disorders, while gut inflammation has been tied to poor systemic health and cardiac inflammation to development of heart disease. One Sentence SummaryChronic, daily inhalation of pod-based e-cigarette aerosols alters the inflammatory state across multiple organ systems in mice.

immunology↗

bioRxiv2019

PARP1 as a biomarker for early detection and intraoperative tumor delineation in epithelial cancers - first-in-human results

Major determining factors for survival of patients with oral, oropharyngeal, and esophageal cancer are early detection, the quality of surgical margins, and the contemporaneous detection of residual tumor. Intuitively, the exposed location at the epithelial surface qualifies these tumor types for utilization of visual aids to assist in discriminating tumor from healthy surrounding tissue. Here, we explored the DNA repair enzyme PARP1 as imaging biomarker and conducted optical imaging in animal models, human tissues and as part of a first-in-human clinical trial. Our data suggests that PARP1 is a quantitative biomarker for oral, oropharyngeal, and esophageal cancer and can be visualized with PARPi-FL, a fluorescently labeled small molecule contrast agent for topical or intravenous delivery. We show feasibility of PARPi-FL-assisted tumor detection in esophageal cancer, oropharyngeal and oral cancer. We developed a contemporaneous PARPi-FL topical staining protocol for human biospecimens. Using fresh oral cancer tissues within 25 min of biopsy, tumor and margin samples were correctly identified with >95% sensitivity and specificity without terminal processing. PARPi-FL imaging can be integrated into clinical workflows, potentially providing instantaneous assessment of the presence or absence of microscopic disease at the surgical margin. Additionally, we showed first-in-human PARPi-FL imaging in oral cancer. In aggregate, our preclinical and clinical studies have the unifying goal of verifying the clinical value of PARPi-FL-based optical imaging for early detection and intraoperative margin assignment.

clinical trials↗