Biology subjects

Nobeli, I.

Publications and source records attributed to Nobeli, I..

7 recordsLinked to original sources

bioRxiv2026

Mitochondrial Optic Atrophy (OPA)1 expression regulates the injury response to neonatal hypoxia-ischaemia.

Neonatal hypoxic-ischaemic encephalopathy is a leading cause of mortality and long-term neurodevelopmental impairment, in which mitochondrial dysfunction is central to injury progression, yet the molecular mechanisms linking mitochondrial dynamics to neuropathology remain incompletely defined. We combined analysis of human developmental transcriptomic datasets with in vitro primary astrocyte models and an established neonatal mouse model of hypoxia-ischaemia (postnatal day 9, Rice-Vannucci model) to investigate the role of the mitochondrial fusion protein Optic Atrophy 1 (OPA1). OPA1 expression and processing were assessed by quantitative PCR and western blotting, mitochondrial function by imaging and Seahorse bioenergetic assays, and mitochondrial DNA content by quantitative PCR in both astrocytes and whole-brain tissue following injury. Hypoxia-ischaemia induced rapid proteolytic processing of OPA1 in the neonatal brain and reduced OPA1 expression in astrocytes following oxygen-glucose deprivation. Genetic reduction of OPA1 in astrocytes resulted in mitochondrial fragmentation, impaired maximal respiration and spare respiratory capacity (p<0.05), and increased susceptibility to hypoxic stress (p<0.01). In vitro, OPA1 loss was associated with significant depletion of mitochondrial DNA (p<0.05), and mitochondrial DNA content was similarly reduced in the neonatal mouse brain 24 hours after hypoxia-ischaemia compared with controls (p<0.05). In contrast, OPA1 overexpression preserved mtDNA levels and significantly reduced in vivo brain tissue loss at 7 days after injury (p<0.05), while improving astrocyte survival following metabolic stress (p<0.001). These findings identify loss of mitochondrial DNA as a previously unrecognised component of mitochondrial pathology in neonatal hypoxic-ischaemic brain injury and demonstrate that OPA1 is a key determinant of mitochondrial integrity and bioenergetic resilience. Targeting OPA1-dependent pathways may represent a novel therapeutic strategy to limit brain injury following birth asphyxia.

neuroscience↗

bioRxiv2022

Using a Whole Genome Co-expression Network to Inform the Functional Characterisation of Predicted Genomic Elements from Mycobacterium tuberculosis Transcriptomic Data

A whole genome co-expression network was created using Mycobacterium tuberculosis transcriptomic data from publicly available RNA-sequencing experiments covering a wide variety of experimental conditions. The network includes expressed regions with no formal annotation, including putative short RNAs and untranslated regions of expressed transcripts, along with the protein-coding genes. These unannotated expressed transcripts were among the best-connected members of the module sub-networks, making up more than half of the hub elements in modules that include protein-coding genes known to be part of regulatory systems involved in stress response and host adaptation. This dataset provides a valuable resource for investigating the role of non-coding RNA, and conserved hypothetical proteins, in transcriptomic remodelling. Based on their connections to genes with known functional groupings and correlations with replicated host conditions, predicted expressed transcripts can be screened as suitable candidates for further experimental validation.

bioinformatics↗

bioRxiv2022

Defining the genes required for survival of Mycobacterium bovis in the bovine host offers novel insights into the genetic basis of survival of pathogenic mycobacteria

Tuberculosis has severe impacts in both humans and animals. Understanding the genetic basis of survival of both Mycobacterium tuberculosis, the human adapted species, and Mycobacterium bovis, the animal adapted species is crucial to deciphering the biology of both pathogens. There are several studies that identify the genes required for survival of M. tuberculosis in vivo using mouse models, however, there are currently no studies probing the genetic basis of survival of M. bovis in vivo. In this study we utilise transposon insertion sequencing in M. bovis to determine the genes required for survival in cattle. We identify genes encoding established mycobacterial virulence functions such as the ESX-1 secretion system, PDIM synthesis, mycobactin synthesis and cholesterol catabolism that are required in vivo. We show that, as in M. tuberculosis, phoPR is required by M. bovis in vivo despite the known defect in signalling through this system. Comparison to studies performed in glycerol adapted species such as M. bovis BCG and M. tuberculosis suggests that there are differences in the requirement for genes involved in cholesterol import (mce4 operon), oxidation (hsd) and detoxification (cyp125). We report good correlation with existing mycobacterial virulence functions, but also find several novel virulence factors, including genes involved in protein mannosylation, aspartate metabolism and glycerol-phosphate metabolism. These findings further extend our knowledge of the genetic basis of survival in vivo in bacteria that cause tuberculosis and provide insight for the development of novel diagnostics and therapeutics. ImportanceThis is the first report of the genetic requirements of an animal adapted member of the MTBC in a natural host. M. bovis has devastating impacts in cattle and bovine tuberculosis is a considerable economic, animal welfare and public health concern. The data highlight the importance of mycobacterial cholesterol catabolism and identifies several new virulence factors. Additionally, the work informs the development of novel differential diagnostics and therapeutics for TB in both human and animal populations.

microbiology↗

bioRxiv2021

Probing differences in gene essentiality between the human and animal adapted lineages of the Mycobacterium tuberculosis complex using TnSeq

Members of the Mycobacterium tuberculosis complex (MTBC) show distinct host adaptations, preferences and phenotypes despite being >99% identical at the nucleic acid level. Previous studies have explored gene expression changes between the members, however few studies have probed differences in gene essentiality. To better understand the functional impacts of the nucleic acid differences between Mycobacterium bovis and Mycobacterium tuberculosis we used the Mycomar T7 phagemid delivery system to generate whole genome transposon libraries in laboratory strains of both species and compared the essentiality status of genes during growth under identical in vitro conditions. Libraries contained insertions in 54% of possible TA sites in M. bovis and 40% of those present in M. tuberculosis, achieving similar saturation levels to those previously reported for the MTBC. The distributions of essentiality across the functional categories were similar in both species. 527 genes were found to be essential in M. bovis whereas 477 genes were essential in M. tuberculosis and 370 essential genes were common in both species. CRISPRi was successfully utilised in both species to determine the impacts of silencing genes including wag31, a gene involved in peptidoglycan synthesis and Rv2182c/Mb2204c, a gene involved in glycerophospholipid metabolism. We observed species specific differences in the response to gene silencing, with the inhibition of expression of Mb2204c in M. bovis showing significantly less growth impact than silencing its ortholog (Rv2182c) in M. tuberculosis. Given that glycerophospholipid metabolism is a validated pathway for antimicrobials, our observations suggest that target vulnerability in the animal adapted lineages cannot be assumed to be the same as the human counterpart. This is of relevance for zoonotic tuberculosis as it implies that the development of antimicrobials targeting the human adapted lineage might not necessarily be effective against the animal adapted lineage. The generation of a transposon library and the first reported utilisation of CRISPRi in M. bovis will enable the use of these tools to further probe the genetic basis of survival under disease relevant conditions.

microbiology↗

bioRxiv2019

flexiMAP: A regression-based method for discovering differential alternative polyadenylation events in standard RNA-seq data

SummaryWe present flexiMAP (flexible Modeling of Alternative PolyAdenylation), a new beta-regression-based method implemented in R, for discovering differential alternative polyadenylation events in standard RNA-seq data. Importantly, flexiMAP allows modeling of multiple known covariates that often confound the results of RNA-seq data analysis. We show, using simulated data, that flexiMAP is very specific and outperforms in sensitivity existing methods, especially at low fold changes. In addition, the tests on simulated data reveal some hitherto unrecognised caveats of existing methods.\n\nAvailabilityThe flexiMAP R package is available at: https://github.com/kszkop/flexiMAP\n\nScripts and data to reproduce the analysis in this paper are available at: https://doi.org/10.5281/zenodo.3238619\n\nContactIrene Nobeli, i.nobeli@bbk.ac.uk

bioinformatics↗

bioRxiv2019

baerhunter: An R package for the discovery and analysis of expressed non-coding regions in bacterial RNA-seq data

SummaryStandard bioinformatics pipelines for the analysis of bacterial transcriptomic data commonly ignore non-coding but functional elements e.g. small RNAs, long antisense RNAs or untranslated regions (UTRs) of mRNA transcripts. The root of this problem is the use of incomplete genome annotation files. Here, we present baerhunter, a method implemented in R, that automates the discovery of expressed non-coding RNAs and UTRs from RNA-seq reads mapped to a reference genome. The core algorithm is part of a pipeline that facilitates downstream analysis of both coding and non-coding features. The method is simple, easy to extend and customize and, in limited tests with simulated and real data, compares favourably against the currently most popular alternative.\n\nAvailabilityThe baerhunter R package is available from: https://github.com/irilenia/baerhunter\n\nContacti.nobeli@bbk.ac.uk

bioinformatics↗

bioRxiv2017

Cell-wall synthesis and ribosome maturation are co-regulated by an RNA switch in Mycobacterium tuberculosis

The success of Mycobacterium tuberculosis as a pathogen relies on the ability to switch between active growth and non-replicating persistence, associated with latent TB infection. Resuscitation promoting factors (Rpfs) are essential for the transition of M. tuberculosis to dormancy and for emergence from the non-replicating persistent state. But these enzymes are double-edged swords, as their ability to degrade the cell wall, is potentially lethal to the bacterium itself. Hence, Rpf expression is tightly regulated. We have identified a novel regulatory element in the 5 untranslated region (UTR) of rpfB. We demonstrate that this element is a transcriptionally regulated RNA switch/riboswitch candidate, which is restricted to pathogenic mycobacteria, suggesting a role in virulence. Moreover, we have used translation start site mapping to re-annotate the RpfB start codon and identified and validated a ribosome binding site that is likely to be targeted by an RpfB antisense RNA. Finally, we show that rpfB is co-transcribed with downstream genes, ksgA and ispE. ksgA encodes a universally conserved methyl transferase involved in ribosome maturation and ispE encodes an essential ATP-dependent kinase involved in cell wall synthesis. This arrangement implies co-regulation of resuscitation, cell wall synthesis and ribosome maturation via the RNA switch. We propose that deregulation of this switch, associated with cell wall synthesis and ribosome function, presents a new target for anti-tuberculosis drug development.\n\nImportanceThis work describes the identification and characterisation of a novel regulatory RNA element/attenuator that controls cell wall synthesis and ribosome function in Mycobacterium tuberculosis, the causative agent of human tuberculosis (TB). By switching between two different conformations, this RNA switch can either enable or inhibit transcription of a tri-cistronic mRNA that encodes a cell-wall remodelling enzyme crucial for activation of latent TB, an RNA methytransferase that is important for ribosome function and a protein kinase essential for early steps in cell wall synthesis. This RNA switch is only present in a subset of pathogenic mycobacteria, and by regulating the expression of three genes associated with classical antimicrobial targets we believe that it offers a novel important target for future anti-tuberculosis drugs.

molecular biology↗