Biology subjects

Rossi, F.

Publications and source records attributed to Rossi, F..

27 records · Page 2Linked to original sources

bioRxiv2021

Illuminati, a novel form of gene expression plasticity in Drosophila neural stem cells

With the aim of developing a genetic instability (GI) sensor in vivo we used the well-established Gal80/Gal4-UAS system combined with a visual GFP marker in Drosophila. We generated a collection of 25 Drosophila lines carrying GAL80 transgenes in different locations in all major chromosomes (X, Y, II, and III). We found low rates of GFP cells in epithelial tissues such as wing discs. In contrast, in larval brains, GFP positive clusters containing neural stem cells- also called neuroblasts (NBs)- and their offspring, were highly frequent. Using genetic and imaging-based approaches, we show that GFP NBs do not result from aneuploidy or mutations in the GAL80 gene, but rather by stochastic repression of GAL80 expression. We named this novel type of gene expression instability Illuminati. Importantly, Illuminati frequency is influenced by environmental and stress conditions. Further, we found that once established, Illuminati can be propagated over many cell cycles.

developmental biology↗

bioRxiv2020

BAP1 activity regulates PcG occupancy and global chromatin condensation counteracting diffuse PCGF3/5-dependent H2AK119ub1 deposition

BAP1 is recurrently mutated or deleted in a large number of diverse cancer types, including mesothelioma, uveal melanoma and hepatocellular cholangiocarcinoma. BAP1 is the catalytic subunit of the Polycomb Repressive De-Ubiquitination complex (PR-DUB) which removes PRC1 mediated H2AK119ub1. We and others have shown that H2AK119ub1 is essential for maintaining transcriptional repression and contributes to PRC2 chromatin recruitment. However, the precise relationship between BAP1 and PRC1 remains mechanistically elusive. Using embryonic stem cells, we show that a major function of BAP1 is to restrict H2AK119ub1 deposition to target sites. This increases the stability of PcG complexes with their targets and prevents diffuse accumulation of H2AK119ub1 and H3K27me3 modifications. Loss of BAP1 results in a broad increase in H2AK119ub1 levels that are primarily dependent on PCGF3/5-PRC1 complexes with a mechanism that is reminiscent of X-chromosome inactivation. Increased genome-wide H2AK119ub1 levels titrates away PRC2 from its targets and stimulates diffuse H3K27me3 accumulation across the genome. This decreases the activity of PcG repressive machineries at physiological targets and induces a general compaction of the entire chromatin. Our findings provide evidences for a unifying model that resolves the apparent contradiction between BAP1 catalytic activity and its role in vivo, uncovering molecular vulnerabilities that could be useful for BAP1-related pathologies.

molecular biology↗

bioRxiv2020

Development of a Coronavirus Disease 2019 Nonhuman Primate Model Using Airborne Exposure

Airborne transmission is predicted to be a prevalent route of human exposure with SARS-CoV-2. Aside from African green monkeys, nonhuman primate models that replicate airborne transmission of SARS-CoV-2 have not been investigated. A comprehensive and comparative evaluation of COVID-19 in African green monkeys, rhesus macaques, and cynomolgus macaques following airborne exposure to SARS-CoV-2 was performed to define parameters critical to disease progression and the extent to which they correlate with human COVID-19. Respiratory abnormalities and viral shedding were noted for all animals, indicating successful infection. Cynomolgus macaques developed fever, and thrombocytopenia was measured for African green monkeys and rhesus macaques. Type II pneumocyte hyperplasia and alveolar fibrosis were more frequently observed in lung tissue from cynomolgus macaques and African green monkeys. The data indicate that, in addition to African green monkeys, macaques can be successfully infected by airborne SARS-CoV-2, providing viable macaque natural transmission models for medical countermeasure evaluation. One Sentence SummaryNonhuman primates develop COVID-19 following airborne virus exposure.

microbiology↗

bioRxiv2019

Multifaceted diversity traits of crucial microbial groups in biological soil crusts promote soil multifunctionality

AbstractsMicrobial diversity is one of the most important drivers on ecosystem to maintain the simultaneous performance of functions (multifunctionality, MF) under climatic oscillation. However, existing studies typically consider taxonomic richness or Shannon index at the community level in which relations between diversity and functioning are not highly consistent. To disentangle the underlying linkages in real-world ecosystems, we conducted field investigation on biological soil crusts of Tibetan Plateau and evaluated multiple diversity facets (i.e., richness, evenness, and phylogeny-related trait dissimilarity) of carbon- and nitrogen-fixing functional groups (FGs). Seven crucial variables of soil functioning were also identified to calculate MF. We found that the integrated index, invoking multiple diversity components, was a stronger predictor on MF than richness. Moreover, the divergent performance of different diversity facets determined the idiosyncratic diversity effect of each FG on the MF. Namely, richness was the dominant factor for diazotrophs to maximize MF, whereas phylogenetic dissimilarity was the most important one for phototrophs. The heterogeneity among the focal FGs derived from the significant differentiation of the extent of multifunctional redundancy. Collectively, we speculated that the multifaceted diversity pattern depicts the response ability of crucial FGs by which biocrusts stabilize MF under environmental perturbation. Taken together, our results provided a perspective to bridge the gap between taxonomic and trait-based approaches for elucidating the biodiversity-ecosystem functioning relationship, and could ultimately help to boost the practices of dryland management against global change.

ecology↗

bioRxiv2019

Quantitative PCR (qPCR) vs culture-dependent detection to assess honey contamination by Paenibacillus larvae

The detection/quantification in honey of spores of the bacterial pathogen Paenibacillus larvae, the etiological agent of the American Foulbrood (AFB) infectious disease of honey bee, represents a useful diagnostic tool to identify apiaries at risk of infection and carry out focused prevention measures. Plate count is currently the recommended method used to analyze presence and number of spores for this pathogen. However, its validity needs to be re-assessed since P. larvae field strains have a low rate of germination in culture media.\n\nTherefore, in this study, culture-dependent P. larvae detection/quantification was compared with quantitative PCR (qPCR) based analysis for 139 honey samples collected in 2017 and 2018 from as many apiaries in the Abruzzo region. According to qPCR based detection, 58.27% samples were positive for P. larvae, while only 33.8 % samples were positive by plate count.\n\nMoreover, the levels of contamination with the two methods differed for most samples. Potential false positives were obtained by plate count for 12.9% samples that were negative with the qPCR test. On the other hand, 26.6% samples were culture negative but qPCR positive, suggesting that not all the field strains were able to develop in plate. This was confirmed by obtaining P. larvae growth from those samples after supplementing the medium with germination stimulants.\n\nResults strongly suggested the necessity to improve culture methods or replace them with molecular detection/quantification for a more reliable AFB risk estimation.

microbiology↗

bioRxiv2019

Pathogenic potential of Hic1 expressing cardiac stromal progenitors

The cardiac stroma contains multipotent mesenchymal progenitors. However, lineage relationships within cardiac stromal cells are still poorly understood. Here, we identify heart-resident PDGFRa+ Sca-1+ cells as cardiac Fibro/Adipogenic Progenitors (cFAPs) and show that they respond to ischemic damage by generating fibrogenic cells. Pharmacological blockade of this differentiation step with an anti-fibrotic tyrosine kinase inhibitor decreases post-myocardial infarction (MI) remodeling and leads to improvements in heart function. In the undamaged heart, activation of cFAPs through lineage-specific deletion of the quiescence factor Hic1 reveals additional pathogenic potential, causing fibro-fatty infiltration of the myocardium and driving major pathological features of Arrhythmogenic Cardiomyopathy (AC). HighlightsO_LIA subpopulation of PDGFRa+, Sca-1+ cells, previously considered to be a sub-type of cardiac fibroblasts, are multipotent mesenchymal progenitors, C_LIO_LICardiac damage triggers the differentiation of PDGFRa+ Sca-1+ cells into Sca-1- cells expressing a fibrogenic transcriptional programme, C_LIO_LIBlockade of the cFAP-to-fibroblast transition by Nilotinib ameliorated cardiac dysfunction post-MI and modulated cardiac remodelling. C_LIO_LIStudies performed on a model of experimentally-induced AC confirmed that cFAPs are a source of both cardiac fibroblasts and adipocytes in vivo. C_LIO_LIConversely, in the undamaged heart, activation of cFAPs by means of lineage-specific deletion of transcription factor Hic1, resulted in fibro/fatty cardiac degeneration and pathological alterations reminiscent of AC. Collectively, our findings show that a proportion of what are commonly termed "fibroblasts" are actually multipotent mesenchymal progenitors that contribute to different forms of cardiac degeneration depending on the damage setting. C_LI

cell biology↗

bioRxiv2018

Carbapenem-resistant Pseudomonas aeruginosa bloodstream infection: in vitro synergy, virulence and clinical outcome

In the current study carbapanem-resistant P. aeruginosa bloodstream infection (CRPA-BSI) was associated with high 14-day mortality. Although, highly resistant to meropenem, half of the isolates achieved in vitro synergy with the combination of meropenem with colistin, and the patients that received this combination therapy showed a tendency towards lower mortality. Our strains did not carry exoU gene, on the other hand, patients with CRPA-BSI caused by strains harboring gene lasB evolved more frequent to death.

microbiology↗

bioRxiv2017

Detecting pathogen exposure during the non-symptomatic incubation period using physiological data

Early pathogen exposure detection allows better patient care and faster implementation of public health measures (patient isolation, contact tracing). Existing exposure detection most frequently relies on overt clinical symptoms, namely fever, during the infectious prodromal period. We have developed a robust machine learning based method to better detect asymptomatic states during the incubation period using subtle, sub-clinical physiological markers. Starting with high-resolution physiological waveform data from non-human primate studies of viral (Ebola, Marburg, Lassa, and Nipah viruses) and bacterial (Y. pestis) exposure, we processed the data to reduce short-term variability and normalize diurnal variations, then provided these to a supervised random forest classification algorithm and post-classifier declaration logic step to reduce false alarms. In most subjects detection is achieved well before the onset of fever; subject cross-validation across exposure studies (varying viruses, exposure routes, animal species, and target dose) lead to 51h mean early detection (at 0.93 area under the receiver-operating characteristic curve [AUCROC]). Evaluating the algorithm against entirely independent datasets for Lassa, Nipah, and Y. pestis exposures un-used in algorithm training and development yields a mean 51h early warning time (at AUCROC=0.95). We discuss which physiological indicators are most informative for early detection and options for extending this capability to limited datasets such as those available from wearable, non-invasive, ECG-based sensors.

physiology↗

bioRxiv2017

Drosophila larval brain neoplasms present tumour-type dependent genome instability

Single nucleotide polymorphisms (SNPs) and copy number variants (CNVs) are found at different rates in human cancer. To determine if these genetic lesions appear in Drosophila tumours we have sequenced the genomes of 17 malignant neoplasms caused by mutations in l(3)mbt, brat, aurA, or lgl. We have found CNVs and SNPs in all the tumours. Tumour-linked CNVs range between 11 and 80 per sample, affecting between 92 and 1546 coding sequences. CNVs are in average less frequent in l(3)mbt than in brat lines. Nearly half of the CNVs fall within the 10 to 100Kb range, all tumour samples contain CNVs larger that 100 Kb and some have CNVs larger than 1Mb. The rates of tumour-linked SNPs change more than 20-fold depending on the tumour type: late stage brat, l(3)mbt, and aurA and lgl lines present median values of SNPs/Mb of exome of 0.16, 0.48, and 3.6, respectively. Higher SNP rates are mostly accounted for by C>A transversions, which likely reflect enhanced oxidative stress conditions in the affected tumours. Both CNVs and SNPs turn over rapidly. We found no evidence for selection of a gene signature affected by CNVs or SNPs in the cohort. Altogether, our results show that the rates of CNVs and SNPs, as well as the distribution of CNV sizes in this cohort of Drosophila tumours are well within the range of those reported for human cancer. Genome instability is therefore inherent to Drosophila malignant neoplastic growth at a variable extent that is tumour type dependent.\n\nAUTHOR SUMMARYDrosophila models of malignant growth can help to understand the molecular mechanisms of malignancy. These models are known to exhibit some of the hallmarks of cancer like sustained growth, immortality, metabolic reprogramming, and others. However, it is currently unclear if these fly models are affected by genome instability, which is another hallmark of many human malignant tumours. To address this issue we have sequenced and analysed the genomes of a cohort of seventeen fly tumour samples. We have found that genome instability is a common trait of Drosophila malignant tumours, which occurs at an extent that is tumour-type dependent, at rates that are similar to those of different human cancers.

cancer biology↗