Biology subjects

Munteanu, A.

Publications and source records attributed to Munteanu, A..

7 recordsLinked to original sources

bioRxiv2024

Novel 3D Approach to Model Non-Alcoholic Fatty Liver Disease using human Pluripotent Stem Cells

Background and aimsNon-alcoholic fatty liver disease (NAFLD) is a major health care challenge and new therapies are urgently needed. However, the mechanisms underlying disease remain to be understood. Indeed, studying NAFLD remains challenging due to the lack of model systems recapitulating the different aspects of the human pathology. Human induced pluripotent stem cells (hiPSCs) offer a unique opportunity to address this limitation since they can be differentiated into large quantity of liver cells. Here, we took advantage of hiPSCs to develop a multi-cellular platform mimicking the complex interplays involved in NAFLD progression. MethodshiPSCs-derived hepatocyte like cells (HLCs), cholangiocytes, stellate cells, and macrophages were co-cultured in a collagen-based 3D system to reproduce the liver microenvironment. Fatty acid treatments led to a NAFLD phenotype involving cell-cell interactions which were investigated by transcriptomic and functional analyses. ResultsHepatic cells were grown up to 4weeks in 3D, retaining key functions and markers. Importantly, co-cultured cells spontaneously reorganised into physiologically relevant connections: HLCs arranged around biliary structures, which established contacts with stellate cells, while macrophages organised around HLCs. Fatty acid treatments induced steatosis and lipotoxicity in HLCs. Furthermore, fat-laden HLCs prompted a non-parenchymal cells response altering tissue architecture. ConclusionsOur multicellular platform provides a new approach to model interactions between human hepatic cells during NAFLD progression. Such approach has the potential to investigate the sequential events driving chronic liver diseases, including hepatocellular injury, inflammation and fibrosis. Furthermore, our system provides a unique and urgently needed tool to investigate the molecular mechanisms associated with NAFLD and ultimately to validate new targets for therapeutics development. List of abbreviationsCOs, cholangiocytes organoids; FFA, free fatty acids; hiPSCs, human induced pluripotent stem cells; HLCs, hepatocyte like cells; HSCs, hepatic stellate cells; M0, hiPSCs-derived macrophages; NAFLD, non-alcoholic fatty liver disease; NPCs, non-parenchymal cells; OA, oleic acid; PA, palmitic acid.

cell biology↗

bioRxiv2022

Population dynamics of free-roaming dogs in Europe and implications for population control

Changes in free-roaming dog population size are important indicators of the effectiveness of dog population management. Assessing the effectiveness of different management methods also requires estimating the processes that change population size, such as the rates of recruitment into and removal from a population. This is one of the first studies to quantify the size, rates of recruitment and removal, and health and welfare status of free-roaming dog populations in Europe. We determined the size, dynamics, and health status of free-roaming dog populations in Pescara, Italy, and Lviv, Ukraine, over a 15-month study period. Both study populations had ongoing dog population management through catch-neuter-release and sheltering programmes. Average monthly apparent survival probability was 0.93 (95% CI 0.81-1.00) in Pescara and 0.93 (95% CI 0.84-0.99) in Lviv. An average of 7 dogs km-2 were observed in Pescara and 40 dogs km-2 in Lviv. Per capita entry probabilities varied between 0.09 and 0.20 in Pescara, and 0.12 and 0.42 in Lviv. In Lviv, detection probability was lower on weekdays (odds ratio: 0.74, 95% CI 0.53-0.96) and higher on market days (odds ratio: 2.58, 95% CI 1.28-4.14), and apparent survival probability was lower in males (odds ratio: 0.25, 95% CI 0.03-0.59). Few juveniles were observed in the study populations, indicating that recruitment may be occurring by movement between dog subpopulations (e.g. from local owned or neighbouring free-roaming dog populations), with important consequences for population control. This study provides important data for planning effective dog population management and for informing population and infectious disease modelling. The results emphasise the importance of dog population management efforts that encourage responsible ownership through reduced abandonment and cover the entire city to reduce the risk of dog movement between sections of the city hindering management efforts.

ecology↗

bioRxiv2022

ClustAssess: tools for assessing the robustness of single-cell clustering

The transition from bulk to single-cell analyses refocused the computational challenges for high-throughput sequencing data-processing. The core of single-cell pipelines is partitioning cells and assigning cell-identities; extensive consequences derive from this step; generating robust and reproducible outputs is essential. From benchmarking established single-cell pipelines, we observed that clustering results critically depend on algorithmic choices (e.g. method, parameters) and technical details (e.g. random seeds). We present ClustAssess, a suite of tools for quantifying clustering robustness both within and across methods. The tools provide fine-grained information enabling (a) the detection of optimal number of clusters, (b) identification of regions of similarity (and divergence) across methods, (c) a data driven assessment of optimal parameter ranges. The aim is to assist practitioners in evaluating the robustness of cell-identity inference based on the partitioning, and provide information for choosing robust clustering methods and parameters. We illustrate its use on three case studies: a single-cell dataset of in-vivo hematopoietic stem and progenitors (10x Genomics scRNA-seq), in-vitro endoderm differentiation (SMART-seq), and multimodal in-vivo peripheral blood (10x RNA+ATAC). The additional checks offer novel viewpoints on clustering stability, and provide a framework for consistent decision-making on preprocessing, method choice, and parameters for clustering.

bioinformatics↗

bioRxiv2021

Assessing the impact of free-roaming dog population management through systems modelling

Free-roaming dogs can present significant challenges to public health, wildlife conservation, and livestock production. Their own welfare may also be a concern, as free-roaming dogs can experience poor health and welfare. Dog population management is widely conducted to mitigate these issues. To ensure efficient use of resources, it is critical that effective, cost-efficient, and high-welfare strategies are identified. The dog population comprises distinct subpopulations characterised by their restriction status and level of ownership, but the assessment of dog population management often fails to consider the impact of the interaction between subpopulations on management success. We present a system dynamics model that incorporates an interactive and dynamic system of dog subpopulations. We identify that methods incorporating both fertility control and responsible ownership interventions (a reduction in abandonment and an increase in shelter adoptions) have the greatest potential to reduce free-roaming dog population sizes over longer periods of time, whilst being cost-effective and improving overall welfare. We suggest that future management should be applied at high levels of coverage and should target all sources of population increase, such as abandonment, births, and free-roaming owned dogs, to ensure effective and cost-efficient reduction in free-roaming dog numbers.

zoology↗

bioRxiv2021

Public attitudes towards free-roaming dogs and dog ownership practices in Bulgaria, Italy, and Ukraine

Overabundant, free-roaming dog populations are associated with risks to public health, livestock losses, wildlife conservation, and dog health and welfare. Dog population management is conducted to mitigate these issues. Assessing dog population management strategies is important to determine their effectiveness, efficiency, and long-term impact. It is essential to also determine how the behaviour and outlook of local communities may influence the efficacy of dog population management. This study aimed to determine public attitudes towards free-roaming dogs and their management and describe dog ownership practices in three European countries using an online questionnaire survey. This study found that most surveyed respondents wanted to see a reduction in free-roaming dog numbers, and felt that this should be achieved through sheltering, catch-neuter-release, and by controlling the breeding of owned dogs. This questionnaire also identified significant associations between public attitudes and dog ownership practices with gender, religious beliefs, age, education level, reason for dog ownership, previous experience with free-roaming dogs, and country of residence. Respondents who identified as: (i) being male, (ii) holding religious beliefs, (iii) owning dogs for practical reasons, (iv) being young, and (v) having no schooling or primary education had a lower probability of neutering and a higher probability of allowing dogs to roam. Respondents who identified as: (i) being female, (ii) feeling threatened by free-roaming dogs, (iii) being older, and (iv) having more education had a higher probability of answering that an increase in free-roaming dog numbers should be prevented. These findings can help to inform future dog population management interventions in these countries and highlight the importance of considering local public attitudes and dog ownership practices in the development of effective dog population management approaches. Including these social factors will ensure that both the community and organisations involved in dog population management work cohesively towards a shared goal.

ecology↗

bioRxiv2018

Deciphering human ribonucleoprotein regulatory networks

RNA-binding proteins (RBPs) control and coordinate each stage in the life cycle of RNAs. Although in vivo binding sites of RBPs can now be determined genome-wide, most studies typically focused on individual RBPs. Here, we examined a large compendium of 114 high-quality transcriptome-wide in vivo RBP-RNA cross-linking interaction datasets generated by the same protocol in the same cell line and representing 64 distinct RBPs. Comparative analysis of categories of target RNA binding preference, sequence preference, and transcript region specificity was performed, and identified potential posttranscriptional regulatory modules, i.e. specific combinations of RBPs that bind to specific sets of RNAs and targeted regions. These regulatory modules encoded functionally related proteins and exhibited distinct differences in RNA metabolism, expression variance, as well as subcellular localization. This integrative investigation of experimental RBP-RNA interaction evidence and RBP regulatory function in a human cell line will be a valuable resource for understanding the complexity of post-transcriptional regulation.

genomics↗

bioRxiv2018

SSMART: Sequence-structure motif identification for RNA-binding proteins

MotivationRNA-binding proteins (RBPs) regulate every aspect of RNA metabolism and function. There are hundreds of RBPs encoded in the eukaryotic genomes, and each recognize its RNA targets through a specific mixture of RNA sequence and structure properties. For most RBPs, however, only a primary sequence motif has been determined, while the structure of the binding sites is uncharacterized.\n\nResultsWe developed SSMART, an RNA motif finder that simultaneously models the primary sequence and the structural properties of the RNA targets sites. The sequence-structure motifs are represented as consensus strings over a degenerate alphabet, extending the IUPAC codes for nucleotides to account for secondary structure preferences. Evaluation on synthetic data showed that SSMART is able to recover both sequence and structure motifs implanted into 3 UTR-like sequences, for various degrees of structured/unstructured binding sites. In addition, we successfully used SSMART on high-throughput in vivo and in vitro data, showing that we not only recover the known sequence motif, but also gain insight into the structural preferences of the RBP.\n\nAvailabilitySSMART is freely available at https://ohlerlab.mdc-berlin.de/software/SSMART_137/\n\nContactuwe.ohler@mdc-berlin.de

bioinformatics↗