Biology subjects

Ferrari, F.

Publications and source records attributed to Ferrari, F..

13 recordsLinked to original sources

bioRxiv2026

Dairy wastewater grease stabilizes in situ mesophilic biomethanation for H2-to-CH4 conversion

Power-to-Gas technologies are emerging as a key strategy to integrate surplus renewable electricity into energy systems, through the conversion of green hydrogen into methane. However, the practical implementation of biological in situ biomethanation is still constrained by operational and design requirements that are incompatible with most existing anaerobic digestion infrastructures. This study demonstrates a stable and efficient mesophilic (37{degrees}C) in situ biomethanation process driven by substrate-induced microbial selection rather than relying on continuous hydrogen supply. Anaerobic digesters co-digesting sewage sludge from a wastewater treatment plant with lipid-rich greases recovered from dairy wastewater developed a pre-adapted hydrogenotrophic consortium capable of effective CO2-H2 conversion under mesophilic conditions. Long-term operation confirmed the robustness and persistence of this microbial structure. Upon H2 addition, methane concentrations up to 82 % were achieved under atmospheric pressure, without biogas recirculation, with hydrogen-to-methane conversion efficiencies up to 90% and methane productivities of 1.64 NLCH4.L-1d-1. 16SrRNA-based microbial community analysis revealed that dairy grease co-digestion selectively enriched hydrogenotrophic methanogens, particularly Methanospirillum, together with syntrophic fatty-acid-degrading bacteria such as Syntrophomonas, promoting efficient interspecies hydrogen transfer. Importantly, the lipid co-substrate enabled the establishment and long-term stability of the hydrogenotrophic pathway independently of hydrogen availability, mitigating challenges associated with intermittent renewable energy supply. Overall, these findings challenge the common reliance on thermophilic conditions, continuous hydrogen input, pressurization, and gas recirculation in in situ biomethanation, demonstrating that substrate-driven microbial selection can replace conventional engineering requirements such as thermophilic operation or reactor modifications, providing a simpler and scalable strategy for mesophilic in situ biomethanation. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=120 SRC="FIGDIR/small/731101v1_ufig1.gif" ALT="Figure 1"> View larger version (30K): org.highwire.dtl.DTLVardef@c62086org.highwire.dtl.DTLVardef@1813ed6org.highwire.dtl.DTLVardef@4462bcorg.highwire.dtl.DTLVardef@1ae2cfb_HPS_FORMAT_FIGEXP M_FIG Graphical Abstract C_FIG Highlights- Lipid-assisted co-digestion promotes stable biogas and biomethane production - Dairy wastewater greases enable mesophilic in situ biomethanation - An enriched hydrogenotrophic methanogenic consortium yields >82% CH4 - 70-90% H2-to-CH4 conversion efficiency under mesophilic, unpressurized conditions - Substrate-driven microbial selection enables in situ biomethanation in WWTP digesters

bioengineering↗

bioRxiv2024

Biochemical properties of chromatin domains define genome compartmentalization

Chromatin three-dimensional (3D) organization inside the cell nucleus determines the separation of euchromatin and heterochromatin domains. Their segregation results in the definition of active and inactive chromatin compartments, whereby the local concentration of associated proteins, RNA and DNA results in the formation of distinct subnuclear structures. Thus, chromatin domains spatially confined in a specific 3D nuclear compartment are expected to share similar epigenetic features and biochemical properties, in terms of accessibility and solubility. Based on this rationale, we developed the 4f-SAMMY-seq to map euchromatin and heterochromatin based on their accessibility and solubility, starting from as little as 10,000 cells. Adopting a tailored bioinformatic data analysis approach we reconstruct also their 3D segregation in active and inactive chromatin compartments and sub-compartments, thus recapitulating the characteristic properties of distinct chromatin states. A key novelty is the capability to map both the linear segmentation of open and closed chromatin domains, as well as their 3D compartmentalization in one single experiment.

genomics↗

bioRxiv2023

Risk and loss aversion and attitude to COVID and vaccines in anxious individuals

Anxious individuals are known to show impaired decision-making in economic gambling task and in everyday life decisions. This impairment can be due to aversion to uncertainty about outcomes (risk aversion) and/or aversion to negative outcomes (loss aversion). We investigate how non-clinical individuals with high levels of Generalised Anxiety Disorder (GAD) (N = 54) behave compared to less anxious subjects (N = 61) in a gambling decision-making task delivered online and designed to separate the distinct influences of risk and loss aversion on decision-making. By modelling subjects choices using computational models derived from Prospect Theory and fitted using Hierarchical Bayesian methods, we estimate individual levels of risk and loss aversion. Moreover we analyse the reaction times and choice data using Hierarchical Drift Diffusion Models (HDDMs). We also link estimates of these parameters to individual propensity to risk averse behaviours during the COVID pandemic, like wearing safer types of face masks, or completing a COVID vaccination course. We report increased loss aversion in individuals with increased level of GAD compared to less anxious individuals and no differences in risk aversion. The HDDM analysis suggests that high anxiety subjects have a reduced bias towards gambling in trials where there is a risk to loose points, also consistent with them being loss averse. We also report no links between risk and loss aversion and attitudes towards COVID and vaccines. These results shed new light on the interplay of anxiety and risk and loss aversion and they can provide useful directions for clinical intervention.

pathology↗

bioRxiv2022

Bub1 availability limits the Spindle Assembly Checkpoint signaling strength of human kinetochores

During mitosis, unattached kinetochores in a dividing cell signal to the Spindle Assembly Checkpoint to delay anaphase onset and prevent chromosome missegregation 1-4. The signaling activity of these kinetochores and the likelihood of chromosome missegregation both depend on the amount of SAC signaling proteins that each kinetochore recruits 5-8. Therefore, factors that control SAC protein recruitment to signaling kinetochores must be thoroughly understood. Phosphoregulation of kinetochore and SAC signaling proteins emerging from the concerted action of many kinases and phosphatases is a major determinant of SAC protein recruitment to signaling kinetochores 9. Whether the abundance of SAC proteins also influences their recruitment and signaling activity at human kinetochores has not been studied 8, 10. Here, we reveal that the low cellular abundance of the SAC signaling protein Bub1 limits kinetochore recruitment of Bub1 and BubR1 and reduces the SAC signaling activity of the kinetochore. Conversely, Bub1 overexpression results in higher protein recruitment and SAC activity producing longer delays in anaphase onset. We also find that the number of SAC proteins recruited by a signaling kinetochore is inversely correlated with the total number of signaling kinetochores in the cell. This correlation likely arises from the competition among the signaling kinetochores to recruit from a limited pool of signaling proteins. The inverse correlation between the number of signaling kinetochores in the cell and the signaling activity of individual kinetochores may allow the dividing cell to prevent the large number of signaling kinetochores in prophase from generating an unnecessarily large signal, while enabling the last unaligned kinetochore to signal at the maximum possible strength.

cell biology↗

bioRxiv2022

Health hazards posed by ionizing radiation to human space missions and newly developing methodologies to investigate them

Ionizing radiation is one of the main threats to human space exploration beyond low Earth orbit (BLEO). It is thus of primary importance to determine safe career dose limits for astronauts involved in BLEO missions. In the first part of this work it is shown how the methods of physics and statistics can contribute to its solution. The average equivalent doses received by a hypothetical human crew are established using the data of several robotic missions to the Moon and to Mars. The probabilities of the occurrence of deterministic effects due to radiation that could impair the success of a mission or lower the life expectancy of astronauts are evaluated with the help of a statistical analysis. In the last part of this work it is argued that the use of the so-called 3D models or organoids combined with the methods of precision oncology and molecular medicine could be a good candidate of a strategy in order to predict the insurgence of stochastic effects in humans. On one side, organoids recapitulate several features of the real human organs and their in vivo surroundings. On the other side, we argue with a case study that precision oncology and molecular medicine are able to provide a deeper insight of the onset of cancer following irradiation in space.

biophysics↗

bioRxiv2021

Leveraging three-dimensional chromatin architecture for effective reconstruction of enhancer-target gene regulatory network

A growing amount of evidence in literature suggests that germline sequence variants and somatic mutations in non-coding distal regulatory elements may be crucial for defining disease risk and prognostic stratification of patients, in genetic disorders as well as in cancer. Their functional interpretation is challenging because genome-wide enhancer-target gene (ETG) pairing is an open problem in genomics. The solutions proposed so far do not account for the most updated knowledge on chromatin three-dimensional (3D) architecture, which is organized in a hierarchy of structural domains. Here we introduce a paradigm shift based on the definition of multi-scale structural chromatin domains, integrated in a statistical framework to define ETG pairs. In this work i) we develop a computational and statistical framework to reconstruct a comprehensive ETG regulatory network leveraging functional genomics data; ii) we demonstrate that the incorporation of chromatin 3D architecture information improves ETG pairing accuracy; and iii) we use multiple experimental datasets to extensively benchmark our method against previous solutions for the genome-wide reconstruction of ETG pairs. This solution will facilitate the annotation and interpretation of sequence variants in distal non-coding regulatory elements. We expect this to be especially helpful in clinically oriented applications of whole genome sequencing in cancer and undiagnosed genetic diseases research.

genomics↗

bioRxiv2020

A ChIC solution for ChIP-seq quality assessment

Despite the widespread adoption of the ChIP-seq technique, there is still no consensus on quality assessment procedures. Quantitative metrics previously proposed in literature are not always effective in discriminating the success or failure of an experiment, thus hampering objectivity and reproducibility of quality control. Here we introduce ChIC, a new framework for ChIP-seq data quality assessment that overcomes the limitations of previous solutions. ChIC is the first method for ChIP-seq quality control directly considering the enrichment profile shape, thus achieving good performances on ChIP targets yielding sharp and broad peaks alike. We integrate a comprehensive set of quality control metrics into one single score reliably summarizing the sample quality. The ChIC score is based on a machine learning classifier trained on a compendium with thousands of ChIP-seq profiles, which can also be used as a reference for easier evaluation of new datasets. ChIC is implemented as a user-friendly R/Bioconductor package.

bioinformatics↗

bioRxiv2020

AutoRELACS: Automated Generation And Analysis Of Ultra-parallel ChIP-seq

Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is a method used to profile protein-DNA interactions genome-wide. RELACS (Restriction Enzyme-based Labeling of Chromatin in Situ) is a recently developed ChIP-seq protocol that deploys a chromatin barcoding strategy to enable standardized and high-throughput generation of ChIP-seq data. The manual implementation of RELACS is constrained by human processivity in both data generation and data analysis. To overcome these limitations, we have developed AutoRELACS, an automated implementation of the RELACS protocol using the liquid handler Biomek i7 workstation. We match the unprecedented processivity in data generation allowed by AutoRELACS with the automated computation pipelines offered by snakePipes. In doing so, we build a continuous workflow that streamlines epigenetic profiling, from sample collection to biological interpretation. Here, we show that AutoRELACS successfully automates chromatin barcode integration, and is able to generate high-quality ChIP-seq data comparable with the standards of the manual protocol, also for limited amounts of biological samples.

genomics↗

bioRxiv2020

CHD8 Suppression Impacts on Histone H3 Lysine 36 Trimethylation and Alters RNA Alternative Splicing.

Disruptive mutations in the chromodomain helicase DNA binding protein 8 (CHD8) have been recurrently associated with Autism Spectrum Disorders (ASD). In normal cellular physiology, CHD8 co-purifies with MLL1 and MOF transcriptional activation complex, with elongating RNAPII and directly binds to DNA promoters and enhancers regions, thus a regulatory role in transcriptional initiation and elongation could be postulated. Here we investigated how chromatin landscape reacts to CHD8 suppression by analyzing a panel of histone modifications in induced pluripotent stem cell-derived neural progenitors. We interrogated transcriptionally active and repressed regions, as well as active and poised enhancers. CHD8 suppression led to significant reduction (47.82%) in histone H3K36me3 peaks at gene bodies, particularly impacting on transcriptional elongation chromatin states. H3K36me3 reduction specifically affects highly expressed, CHD8-bound genes. Histone H3K36me3 reduction associated to CHD8-suppression does not functionally impact on global transcriptional levels, but correlated with altered alternative splicing patterns of [~] 2000 protein coding genes implicated in "RNA splicing", "mitotic cell cycle phase transition" and "mRNA processing", especially affecting alternative first exon and exon skipping events. In summary, our results point toward broad molecular consequences of CHD8 suppression, implicating altered histone deposition/maintenance and RNA processing regulation as important regulatory processes in ASD.

genetics↗

bioRxiv2020

DOT1L Methyltransferase Activity Preserves SOX2-Enhancer Accessibility And Prevents Activation of Repressed Genes In Murine Stem Cells

BackgroundDuring cellular differentiation, the chromatin landscape changes dynamically and contributes to the activation of cell-type specific transcriptional programs. Disruptor of telomeric silencing 1-like (DOT1L) is a histone methyltransferase that mediates mono-, di- and trimethylation of lysine 79 of histone H3 (H3K79me1, 2, 3). Its enzymatic activity is critical for driving cellular differentiation into cardiomyocytes, chondrocytes and neurons, from embryonic or other type of stem cells in physiological settings. Ectopic localization of DOT1L in MLL-rearranged leukemias is causative for leukemogenesis and relapse. Little is known about the causal relevance of DOT1L methyltransferase activity in the global chromatin context and how its enzymatic function affects transcriptional and global chromatin states. Recent reports conducted in leukemia cell models have suggested that deposition of H3K79me2 may be critical to preserve histone H3K27 acetylation (ac) and enhancer activity, and to sustain expression of highly transcribed genes. If and to what extent DOT1L affects chromatin states and enhancer activity during physiological differentiation processes is currently unknown. ResultsWe measure global changes of seven histone modifications during the differentiation process via high-throughput and quantitative ChIP-seq in an in-vitro neuronal differentiation model of mouse embryonic stem cells (mESC). We observe that H3K27ac globally decreases, whereas H3K79me2 globally increases during differentiation, while other modifications remain globally unaltered. Pharmacological inhibition of DOT1L in mESC and mESC-derived neural progenitors results in decreased expression of highly transcribed genes and increased expression of normally repressed genes. Acute DOT1L inhibition primes neural progenitors towards a mature differentiation state. Transcriptional downregulation associates with decreased accessibility of enhancers specifically bound by the master regulator SOX2. ConclusionsIn-vitro neuronal differentiation couples with a genome-wide accumulation of H3K79me2, never described previously in mammalian cells. Acute inhibition of DOT1L is sufficient to initiate a defined transcriptional program, which biases the transcriptome of neural progenitor cells towards neuronal differentiation. H3K79me2 is not generally causative for maintaining transcriptional levels at a genome-wide scale. In contrast, DOT1L inactivation reduces the chromatin accessibility of enhancers bound by SOX2 in-vivo, thereby reducing the expression level of a restricted number of genes. Our work establishes that DOT1L activity gates differentiation of progenitors by allowing SOX2-dependent transcription of stemness programs.

genomics↗

bioRxiv2020

ATR expands embryonic stem cell fate potential in response to replication stress

Unrepaired DNA damage during embryonic development can be potentially inherited by a large population of cells. However, the quality control mechanisms that minimize the contribution of damaged cells to developing embryos remain poorly understood. Here, we uncovered an ATR- and CHK1-mediated transcriptional response to replication stress (RS) in ESCs that induces genes expressed in totipotent two-cell (2C) stage embryos and 2C-like cells. This response is mediated by Dux, a multicopy retrogene defining the cleavage-specific transcriptional program in placental mammals. In response to RS, DUX triggers the transcription of 2C-like markers such as murine endogenous retrovirus-like elements (MERVL) and Zscan4. This response can also be elicited by ETAA1-mediated ATR activation in the absence of RS. ATR-mediated activation of DUX requires GSRF1 dependent post-transcriptional regulation of Dux mRNA. Strikingly, activation of ATR expands ESCs fate potential by extending their contribution to both embryonic and extra{-}embryonic tissues. These findings define a novel ATR dependent pathway involved in maintaining genome stability in developing embryos by controlling ESCs fate in response to RS.

cell biology↗

bioRxiv2019

Early Polycomb-target deregulations in Hutchinson-Gilford Progeria Syndrome revealed by heterochromatin analysis

Hutchinson-Gilford progeria syndrome (HGPS) is characterized by the progressive accumulation of progerin, an aberrant form of Lamin A. This leads to chromatin structure disruption, in particular by interfering with Lamina Associated Domains. Although several cellular and molecular alterations have been characterized, it is still unclear how chromatin structural changes translate into premature senescence in HGPS. Moreover, early events in chromatin remodeling have not been detected so far. We developed a new high-throughput sequencing-based method, named SAMMY-seq, for genome-wide characterization of heterochromatin accessibility changes. Using SAMMY-seq, we detected early stage alterations of chromatin structure in HGPS primary fibroblasts. Of note, these structural changes do not disrupt the distribution of H3K9me3 but are associated with site-specific H3K27me3 variations and transcriptional dysregulation of Polycomb target genes. Our results show that SAMMY-seq represents a novel and sensitive tool to characterize heterochromatin alterations. Moreover, we found that the assembly of lamin associated domains is strictly connected to the correct Polycomb repression, rapidly lost in early HGPS pathogenesis.

molecular biology↗

bioRxiv2019

Functional analysis of OCTN2 and ATB0,+ in normal human airway epithelial cells

In human, OCTN2 (SLC22A5) and ATB0,+ (SLC6A14) transporters mediate the uptake of L-carnitine, essential for the transport of fatty acids into mitochondria and the subsequent degradation by {beta}-oxidation. Aim of the present study is to characterize L-carnitine transport in EpiAirway, a 3D organotypic in vitro model of primary human tracheal-bronchial epithelial cells that form a fully differentiated, pseudostratified columnar epithelium at air-liquid interface (ALI) condition. In parallel, Calu-3 monolayers grown at ALI were used as comparison. In EpiAirway, ATB0,+ was highly expressed and functional on the apical side while OCTN2 transporter was active on the basolateral side. Calu-3 cells showed a different pattern of expression and activity for ATB0,+: indeed, L-carnitine uptake on apical side was evident in Calu-3 at 8 days of culture but not in fully differentiated 21d ALI culture. As both ATB0,+ and OCTN2, beyond transporting L-carnitine, have a significant potential as delivery systems for drugs, the identification of these transporters in EpiAirway can open new fields of investigation in the studies of drug inhalation and pulmonary delivery.

cell biology↗