Biology subjects

Ferrari, A.

Publications and source records attributed to Ferrari, A..

32 records · Page 2Linked to original sources

bioRxiv2023

Aster-dependent non-vesicular transport facilitates dietary cholesterol uptake

Intestinal cholesterol absorption is an important contributor to systemic cholesterol homeostasis. Niemann-Pick C1 Like 1 (NPC1L1), the target of the drug ezetimibe (EZ), assists in the initial step of dietary cholesterol uptake. However, how cholesterol moves downstream of NPC1L1 is unknown. Here we show that Aster-B and Aster-C are critical for non-vesicular cholesterol movement in enterocytes, bridging NPC1L1 at the plasma membrane (PM) and ACAT2 in the endoplasmic reticulum (ER). Loss of NPC1L1 diminishes accessible PM cholesterol in enterocytes and abolishes Aster recruitment to the intestinal brush border. Enterocytes lacking Asters accumulate cholesterol at the PM and display evidence of ER cholesterol depletion, including decreased cholesterol ester stores and activation of the SREBP-2 transcriptional pathway. Aster-deficient mice have impaired cholesterol absorption and are protected against diet-induced hypercholesterolemia. Finally, we show that the Aster pathway can be targeted with a small molecule inhibitor to manipulate dietary cholesterol uptake. These findings identify the Aster pathway as a physiologically important and pharmacologically tractable node in dietary lipid absorption. One-Sentence SummaryIdentification of a targetable pathway for regulation of dietary cholesterol absorption

physiology↗

bioRxiv2023

Tetravalent SARS-CoV-2 S1 Subunit Protein Vaccination Elicits Robust Humoral and Cellular Immune Responses in SIV-Infected Rhesus Macaque Controllers

The COVID-19 pandemic has highlighted the need for safe and effective vaccines to be rapidly developed and distributed worldwide, especially considering the emergence of new SARS-CoV-2 variants. Protein subunit vaccines have emerged as a promising approach due to their proven safety record and ability to elicit robust immune responses. In this study, we evaluated the immunogenicity and efficacy of an adjuvanted tetravalent S1 subunit protein COVID-19 vaccine candidate composed of the Wuhan, B.1.1.7 variant, B.1.351 variant, and P.1 variant spike proteins in a nonhuman primate model with controlled SIVsab infection. The vaccine candidate induced both humoral and cellular immune responses, with T- and B cell responses mainly peaking post-boost immunization. The vaccine also elicited neutralizing and cross-reactive antibodies, ACE2 blocking antibodies, and T-cell responses, including spike specific CD4+ T cells. Importantly, the vaccine candidate was able to generate Omicron variant spike binding and ACE2 blocking antibodies without specifically vaccinating with Omicron, suggesting potential broad protection against emerging variants. The tetravalent composition of the vaccine candidate has significant implications for COVID-19 vaccine development and implementation, providing broad antibody responses against numerous SARS-CoV-2 variants.

immunology↗

bioRxiv2022

SARS-CoV-2 S1 Subunit Booster Vaccination Elicits Robust Humoral Immune Responses in Aged Mice

Currently approved COVID-19 vaccines prevent symptomatic infection, hospitalization, and death of the disease. However, the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants raises concerns of reduced vaccine effectiveness and increased risk of infection. Repeated homologous booster in elderly individuals and immunocompromised patients is considered to solve severe form of disease caused by new SARS-CoV-2 variants but cannot protect completely against breakthrough infection. In our previous study we assessed the immunogenicity of an adenovirus-based vaccine expressing SARS-CoV-2-S1 (Ad5.S1) in mice, resulting in that a single immunization with Ad5.S1, via subcutaneously injection or intranasal delivery, induced robust humoral and cellular immune responses [1]. As a follow up study, here we showed that vaccinated mice had high titers of anti-S1 antibodies at one year after vaccination compared to PBS immunized mice. Furthermore, one booster dose of non-adjuvanted recombinant S1Beta (rS1Beta) subunit vaccine was effective in stimulating strong long-lived S1-specific immune responses and inducing significantly high neutralizing antibodies against the Wuhan, Beta, and Delta strain with 3.6- to 19.5-fold change increases. Importantly, the booster dose elicits cross-reactive antibody responses resulting in ACE2 binding inhibition against spike of SARS-CoV-2 variants (Wuhan, Alpha, Beta, Gamma, Delta, Zeta, Kappa, New York, India) as early as two-week post-boost injection, persisting over 28 weeks after a booster vaccination. Interestingly, levels of neutralizing antibodies were correlated with not only level of S1-binding IgG but also level of ACE2 inhibition in the before- and after-booster serum samples. Our findings show that S1 recombinant protein subunit vaccine candidate as a booster has potential to offer cross-neutralization against broad variants, and has important implications for vaccine control of new emerging breakthrough SARS-CoV-2 variants in elderly individuals primed with adenovirus-based vaccine like AZD1222 and Ad26.COV2.S.

microbiology↗

bioRxiv2022

Strandings of loggerhead sea turtles south of the Po River delta: insights from a highly impacted area

The northern Adriatic Sea is an important foraging ground for the loggerhead sea turtle Caretta caretta (Linnaeus, 1758) within the Mediterranean Sea. Here, spatial-temporal patterns of loggerhead sea turtles strandings along a short portion ([~]18 km) of the coast south of the Po River delta (Italy) during a three-year period (2019-2021) were investigated. A total of 244 records (alive, n=7; dead, n=237) were analysed and the curved carapace lengths (CCL, notch to tip, cm) mainly reflected sub-adults (average CCL=55.2 cm; 95% CI= 53.3-57). The month of July was identified as the critical month with the highest number of strandings, mirroring migratory processes toward this area during warmer months. Interaction with the trawl fishery was hypothesized as the main cause of mortality and a small fraction of deaths (6%; n=16) could be linked to boat strikes and net entanglement. The number of stranded turtles*km-1 as well as the absolute number of strandings along the short portion of monitored coast confirmed this area as the most impacted in Italy and perhaps in the whole Mediterranean Sea. This study provides valuable information to improve conservation efforts for this species and highlight that, with all due caution, monitoring stranding events can offer useful insights into the geographic ranges, seasonal distribution, and life history of marine species of conservation interest such as the loggerhead sea turtle.

ecology↗

bioRxiv2022

Updating contextual sensory expectations for adaptive behaviour

The brain has the extraordinary capacity to construct predictive models of the environment by internalizing statistical regularities in the sensory inputs. The resulting sensory expectations shape how we perceive and react to the world; at the neural level, this relates to decreased neural responses to expected than unexpected stimuli ( expectation suppression). Crucially, expectations may need revision as context changes. However, existing research has often neglected this issue. Further, it is unclear whether contextual revisions apply selectively to expectations relevant to the task at hand, hence serving adaptive behaviour. The present fMRI study examined how contextual visual expectations spread throughout the cortical hierarchy as participants update their beliefs. We created a volatile environment with two state spaces presented over separate contexts and controlled by an independent contextualizing signal. Participants attended a training session before scanning to learn contextual temporal associations among pairs of object images. The fMRI experiment then tested for the emergence of contextual expectation suppression in two separate tasks, respectively with task-relevant and task-irrelevant expectations. Behavioural and neural effects of contextual expectation emerged progressively across the cortical hierarchy as participants attuned themselves to the context: expectation suppression appeared first in the insula, inferior frontal gyrus and posterior parietal cortex, followed by the ventral visual stream, up to early visual cortex. This applied selectively to task-relevant expectations. Taken together, the present results suggest that an insular and frontoparietal executive control network may guide the flexible deployment of contextual sensory expectations for adaptive behaviour in our complex and dynamic world. Significance statementThe world is structured by statistical regularities, which we use to predict the future. This is often accompanied by suppressed neural responses to expected compared with unexpected events ( expectation suppression). Crucially, the world is also highly volatile and context-dependent: expected events may become unexpected when the context changes, thus raising the crucial need for belief updating. However, this issue has generally been neglected. By setting up a volatile environment, we show that expectation suppression emerges first in executive control regions, followed by relevant sensory areas, only when observers use their expectations to optimise behaviour. This provides surprising yet clear evidence on how the brain controls the updating of sensory expectations for adaptive behaviour in our ever-changing world.

neuroscience↗

bioRxiv2022

Force-biased nuclear import sets nuclear-cytoplasmic volumetric coupling by osmosis

In eukaryotes, cytoplasmic and nuclear volumes are tightly regulated to ensure proper cell homeostasis. However, the detailed mechanisms underlying nucleus-cytoplasm volumetric coupling remain unknown. Recent evidence supports a primary role of osmotic mechanisms in determining a tight link between nuclear and cytoplasmic volume, but this hypothesis remains largely untested in mammalian cells. We approach the question in single cultured adhering human cells, by jointly measuring cytoplasmic and nuclear volumes, in real time and across cell cycles. Surprisingly, we find that cytoplasmic and nuclear volumes follow different average growth laws: while the cytoplasm grows exponentially, the nucleus grows linearly. Moreover, by combining several experimental perturbations and analyzing a mathematical model including osmotic effects and tension, we conclude that the mechanical forces exerted by the cytoskeleton on the nuclear envelope can strongly affect nucleus-cytoplasm volumetric coupling by biasing nuclear import. Our results unveil how osmo-mechanical equilibrium regulates nuclear size in mammalian cells. One-Sentence SummaryCytoskeletal forces exerted on the nuclear envelope impact on nuclear volume through modulation of force-coupled nucleo-cytoplasmic transport, affecting osmosis.

cell biology↗

bioRxiv2022

SiCoDEA: a simple, fast and complete app for analyzing the effect of individual drugs and their combinations

The administration of combinations of drugs is a method widely used in the treatment of different pathologies as it can lead to an increase in the therapeutic effect and a reduction in the dose compared to the administration of the single drugs. For these reasons, it is of interest to study combinations of drugs and in particular to determine whether a specific combination has a synergistic, antagonistic or additive effect, i.e greater, less than or equal to the effect expected by the sum of the individual drugs. For this purpose, various mathematical models have been developed, which use different methods to evaluate the synergy of a combination of drugs. Most of these methods are based on the Loewe Additivity Principle (Loewe et al., 1953), which has its key step in choosing the model used for predicting the effect of individual drugs. Creating a model for this purpose and calculating its parameters, however, requires a certain level of mathematical and programming knowledge or the use of commercial software. For this purpose, therefore, we have developed an open access and easy to use app that allows to explore different models and to choose the most fitting for the specific experimental data: SiCoDEA (Single and Combined Drug Effect Analysis, https://sicodea.shinyapps.io/shiny/). The data used to test SiCoDEA comes from cell line samples treated with different drug combinations and analyzed through metabolic or viability assays. SiCoDEA is developed through a Shiny interactive and easy-to-use interface (R based). There are five models taken into consideration for the analysis of single drugs and the calculation of combination index. The first is one of the most used, that of the median-effect; while the others are different forms of the log-logistic equation, with two, three and four parameters. The purpose of SiCoDEA is, on the one hand, to provide an easy-to-use tool for analyzing drug combination data and, on the other hand, also to have a view of the various steps and to offer different results based on the model chosen. An important prerequisite in analyzing drug combinations is in fact the dose-response curve calculated for individual drugs. For this purpose, SiCoDEA allows you to view the plots of the individual drugs both to evaluate the distribution of the calculated points and therefore identify any outliers, and to view the curve of the different models taken into consideration and evaluate which one best fits the data. A table showing all the R2 values for the five different models is created with the curve plot. In addition to the type of model, it is also possible to choose between two different normalization methods, one based on the maximum or minimum value and the other on the value calculated at drug concentrations equal to zero. For the chosen options, a plot is then created that shows the trend of the combination index for the different drug combinations and consequently whether it is synergy, antagonism or additivity. Finally, it is possible to export the results in single png files or in a summary report in pdf. SiCoDEA is an open-source app among the most complete and offers more functions even than the famous CompuSyn (Chou et al., 2010), as it allows you to analyze drug curves with different models, rather than just one, and it also allows the analysis of single drug curves.

bioinformatics↗

bioRxiv2022

PIP4K2B is a mechanosensor and induces heterochromatin-driven nuclear softening through UHRF1.

Phosphatidylinositol-5-phosphate (PtdIns5P)-4-kinases (PIP4Ks) are stress-regulated phosphoinositide kinases able to phosphorylate PtdIns5P to PtdIns(4, 5)P2. In cancer patients their expression is typically associated with bad prognosis. Among the three PIP4K isoforms expressed in mammalian cells, PIP4K2B is the one with more prominent nuclear localization. Here, we unveil the role for PIP4K2B as mechanosensor. PIP4K2B protein level, indeed, strongly decreases in cells growing on soft substrates. Its direct silencing or pharmacological inhibition, mimicking cell response to soft, triggers a concomitant reduction of the epigenetic regulator UHRF1 and induces changes in nuclear polarity, nuclear envelope tension and chromatin compaction. This substantial rewiring of the nucleus mechanical state drives YAP cytoplasmic retention and impairment of its activity as transcriptional regulator, finally leading to defects in cell spreading and motility. Since YAP signalling is essential for initiation and growth of human malignancies, our data suggest that potential therapeutic approaches targeting PIP4K2B could be beneficial in the control of the altered mechanical properties of cancer cells.

cell biology↗

bioRxiv2022

Statistical learning is not error-driven

Prediction errors have a prominent role in many forms of learning. For example, in reinforcement learning, agents learn by updating the association between states and outcomes as a function of the prediction error elicited by the event. One paradigm often used to study error-driven learning is blocking. In forward blocking, participants are first presented with stimulus A, followed by outcome X (A[->]X). In the second phase, A and B are presented together, followed by X (AB[->]X). Here, A[->]X blocks the formation of B[->]X, given that X is already fully predicted by A. In backward blocking, the order of phases is reversed. Here, the association between B and X that is formed during the first learning phase of AB[->]X is weakened when participants learn exclusively A[->]X in the second phase. The present study asked the question whether forward and backward blocking occur during visual statistical learning, the largely automatic and incidental learning of the statistical structure of the environment. In a series of studies, using both forward and backward blocking, we observed robust statistical learning of temporal associations among pairs of images. While we found no compelling evidence for forward blocking, we observed reliable backward blocking in visual statistical learning.

neuroscience↗

bioRxiv2021

Immunity to SARS-CoV-2 up to 15 months after infection

BackgroundInformation concerning the longevity of immunity to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) following natural infection may have considerable implications for durability of immunity induced by vaccines. Here, we monitored the SARS-CoV-2 specific immune response in convalescent coronavirus disease-2019 (COVID-19) patients up to 15 months after symptoms onset. MethodsThe levels of anti-spike and anti-receptor binding domain antibodies and neutralizing activities were tested in a total of 188 samples from 136 convalescent patients who experience mild to critical COVID-19. Specific memory B and T cell responses were measured in 76 peripheral blood mononuclear cell samples collected from 54 patients. Twenty-three vaccinated individuals were included for comparison. FindingsFollowing a peak at day 15-28 post-infection, the IgG antibody response and plasma neutralizing titers gradually decreased over time but stabilized after 6 months. Plasma neutralizing activity against G614 was still detected in 87% of the patients at 6-15 months. Compared to G614, the median neutralizing titers against Beta, Gamma and Delta variants in plasma collected at early (15-103 days) and late (9-15 month) convalescence were 16- and 8-fold lower, respectively. SARS-CoV-2-specific memory B and T cells reached a peak at 3-6 months and persisted in the majority of patients up to 15 months although a significant decrease in specific T cells was observed between 6 and 15 months. ConclusionThe data suggest that antiviral specific immunity especially memory B cells in COVID-19 convalescent patients is long-lasting, but some variants of concern, including the fast-spreading Delta variant, may at least partially escape the neutralizing activity of plasma antibodies. FundingEU-ATAC consortium, the Italian Ministry of Health, the Swedish Research Council, SciLifeLab, and KAW.

immunology↗

bioRxiv2021

Harnessing the power of metabarcoding in the ecological interpretation of plant-pollinator DNA data: strategies and consequences of reads filtering

DNA metabarcoding approaches to analyse complex mixtures of pollen has become the standard in pollination biology, especially in the light of recent threats affecting pollination. In spite of the increasing adoption of High Throughput Sequencing (HTS) approaches, these studies generate huge numbers of raw reads, some of which might be associated to false positives or infrequently recorded species with potentially little biological information. If these reads are not discarded (i.e. pruned), they can lead to changes in the ecological findings and lead to biased conclusions. In this study we reviewed 42 papers in the recent pollen DNA metabarcoding literature and focused on the type of pruning applied. We also tested whether the different types of those cut off threshold may leave a mark on the DNA metabarcoding data. To do so, we compared for the first time community composition, species richness and networks of species interactions (i.e. Connectace, Modularity, Connectivity and Shannon entropy) associated with the most relevant ways of treating HTS outputs: no cut (no reads filtering), or cutting levels obtained as proportional 1% of sample total reads, or as fixed amount of 100 reads, or from ROC (Receiver operator characteristic). Results clearly indicated that pruning type shapes species composition and that to apply or not a threshold dramatically impacts ecological indices, potentially increasing the risk of misinterpreting DNA metabarcoding data under an ecological point of view. Given the high methodological heterogeneity from the revised literature, we discuss in what conditions filtering types may be more appropriate, and also recommend to biologically justify the pruning threshold when analysing DNA metabarcoding raw reads, and to develop shared approaches to make future studies more comparable.

ecology↗

bioRxiv2020

Visual motion processing recruits regions selective for auditory motion in early deaf individuals

In early deaf individuals, the auditory deprived temporal brain regions become engaged in visual processing. In our study we tested further the hypothesis that intrinsic functional specialization guides the expression of cross-modal responses in the deprived auditory cortex. We used functional MRI to characterize the brain response to horizontal, radial and stochastic visual motion in early deaf and hearing individuals matched for the use of oral or sign language. Visual motion showed enhanced response in the deaf mid-lateral planum temporale, a region selective to auditory motion as demonstrated by a separate auditory motion localizer in hearing people. Moreover, multivariate pattern analysis revealed that this reorganized temporal region showed enhanced decoding of motion categories in the deaf group, while visual motion-selective region hMT+/V5 showed reduced decoding when compared to hearing people. Dynamic Causal Modelling revealed that the deaf motion-selective temporal region shows a specific increase of its functional interactions with hMT+/V5 and is now part of a large-scale visual motion selective network. In addition, we observed preferential responses to radial, compared to horizontal, visual motion in the deaf right superior temporal cortex region that also show preferential response to approaching/receding sounds in the hearing brain. Overall, our results suggest that the early experience of auditory deprivation interacts with intrinsic constraints and triggers a large-scale reallocation of computational load between auditory and visual brain regions that typically support the multisensory processing of motion information. HighlightsO_LIAuditory motion-sensitive regions respond to visual motion in the deaf C_LIO_LIReorganized auditory cortex can discriminate between visual motion trajectories C_LIO_LIPart of the deaf auditory cortex shows preference for in-depth visual motion C_LIO_LIDeafness might lead to computational reallocation between auditory/visual regions. C_LI

neuroscience↗

bioRxiv2019

Using the past to estimate sensory uncertainty

To form the most reliable percept of the environment, the brain needs to represent sensory uncertainty. Current theories of perceptual inference assume that the brain computes sensory uncertainty instantaneously and independently for each stimulus.\n\nIn a series of psychophysics experiments human observers localized auditory signals that were presented in synchrony with spatially disparate visual signals. Critically, the visual noise changed dynamically over time with or without intermittent jumps. Our results show that observers integrate audiovisual inputs weighted by sensory reliability estimates that combine information from past and current signals as predicted by an optimal Bayesian learner or approximate strategies of exponential discounting\n\nOur results challenge classical models of perceptual inference where sensory uncertainty estimates depend only on the current stimulus. They demonstrate that the brain capitalizes on the temporal dynamics of the external world and estimates sensory uncertainty by combining past experiences with new incoming sensory signals.

neuroscience↗

bioRxiv2018

Partially methylated domains are hypervariable in breast cancer and fuel widespread CpG island hypermethylation

Global loss of DNA methylation and CpG island (CGI) hypermethylation are regarded as key epigenomic aberrations in cancer. Global loss manifests itself in partially methylated domains (PMDs) which can extend up to megabases. However, the distribution of PMDs within and between tumor types, and their effects on key functional genomic elements including CGIs are poorly defined. Using whole genome bisulfite sequencing (WGBS) of breast cancers, we comprehensively show that loss of methylation in PMDs occurs in a large fraction of the genome and represents the prime source of variation in DNA methylation. PMDs are hypervariable in methylation level, size and distribution, and display elevated mutation rates. They impose intermediate DNA methylation levels incognizant of functional genomic elements including CGIs, underpinning a CGI methylator phenotype (CIMP). However, significant repression effects on cancer-genes are negligible as tumor suppressor genes are generally excluded from PMDs. The genomic distribution of PMDs reports tissue-of-origin of different cancers and may represent tissue-specific silent regions of the genome, which tolerate instability at the epigenetic, transcriptomic and genetic level.

cancer biology↗