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Articles by Davide Risso
On Taste In Humans and Other Animals
About The Book About The Author Reviews Are there only five tastes, sweet, salty, sour, bitter, and umami? Why are some so appealing to us while others are what we call acquired tastes? Do other animals perceive tastes in the same way humans do? How did the sense of taste evolve? Should the hotness of chili peppers, the coolness of mint, and the pungency of garlic be considered tastes? What can taste teach us about our health and our environment?
Dolcificare con il pensiero, quanto la percezione gustativa può venire influenzata dalle nostre aspettative?
Il momento in cui assaggiamo qualcosa di dolce sembra quasi magico. È una sequenza lineare, quasi meccanica. Parte dalla lingua, che ci restituisce una sensazione edonica avvolgente e arriva al cervello, che la interpreta come dolce, spesso invogliandoci a desiderarne ancora. Eppure, come spesso accade, la realtà è più sfumata e, forse, ancora più magica.
omicsGMF: a multi-tool for dimensionality reduction, batch correction and imputation in bulk- and single-cell proteomics
Abstract The unprecedented speed and sensitivity of mass spectrometry (MS) unlocked large-scale applications of proteomics and even enabled proteome profiling of single cells. However, this fast-evolving field is hindered by a lack of scalable dimensionality reduction tools that can compensate for substantial batch effects and missingness across MS runs.
A latent activated olfactory stem cell state revealed by single-cell transcriptomic and epigenomic profiling
ArticleOnline now102778Open access 1Department of Statistics, University of California, Berkeley, Berkeley, CA, USA 2Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium 3Molecular Neurobiology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA 4Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA 5Department of Statistical Sciences,...
La matematica del sapore, si può indovinare l’origine di una ricetta dalla combinazione dei suoi ingredienti?
A chi piace cucinare sembrerà quasi automatico, perché spesso è una questione di ore e ore di pratica ed osservazione, aggiungendo particolari ingredienti alla ricetta per sprigionare una combinazione di sapore particolarmente gustosa. La mela e la cannella, il pomodoro con il basilico, le pere con il formaggio, il cacio con il pepe. Se questo è vero in Italia, non sempre però troviamo le medesime accoppiate in altri paesi del mondo.
Abbiamo un sesto senso ‘batterico’? Una nuova scoperta ci illumina sull’asse intestino-cervello
Intestino e cervello, un rapporto sempre più studiato e discusso. E ora uno studio aggiunge un ulteriore tassello. Ma facciamo prima un passo indietro: a partire da Aristotele, l’idea che gli esseri umani posseggano cinque sensi si è radicata sempre più nel tempo. Li conosciamo tutti: il gusto, l’olfatto, l’udito, il tatto e la vista. Sappiamo anche che il cervello riceve, interpreta e rielabora i segnali provenienti da questi sensi, generando risposte appropriate.
Sviluppare una varietà di riso che possa crescere e resistere nello spazio, conosciamo meglio il progetto italiano ‘Moon Rice’
Era il 2022 quando alcuni ricercatori cinesi coltivarono per la prima volta semi di riso in orbita, a bordo della Stazione Spaziale Cinese. Questo cereale non è però l’unico ad essere stato coltivato nello spazio: troviamo anche il grano, la colza, i piselli, il crescione, la lattuga e le zucchine, tra gli altri. Si è persino fermentato un miso, nello spazio.
Perché il gusto del caffè è troppo amaro per alcuni e per altri no? Forse ora abbiamo la risposta
Caffè amaro o caffè zuccherato? In Italia è qualcosa di più di una bevanda popolare. È un rituale sociale radicato, un fenomeno culturale che scandisce la quotidianità e socialità del Paese. Basti pensare come, solamente nei nostri bar, se ne stimi un consumo di 95 milioni di tazzine al giorno: oltre 30 miliardi di tazzine all’anno. Oppure come il mercato degli speciality coffee sia in continua crescita, in particolar modo tra i più giovani.
Fermentare nello spazio? Una pasta di miso prodotta in orbita dimostra che si può fare (e aggiunge anche più sapore)
Fermentare nello spazio non è fantascienza ma realtà. La fermentazione, una delle tendenze più in voga negli ultimi anni, è un processo naturale ad opera di lieviti, batteri o muffe che decompongono composti organici, come zuccheri o proteine, producendo in cambio energia, gas, alcol e una miriade di composti gustativi ed aromatici.
A Latent Activated Olfactory Stem Cell State Revealed by Single Cell Transcriptomic and Epigenomic Profiling
Abstract The olfactory epithelium is one of the few regions of the nervous system that sustains neurogenesis throughout life. Its experimental accessibility makes it especially tractable for studying molecular mechanisms that drive neural regeneration in response to injury. In this study, we used single-cell sequencing to identify the transcriptional cascades and epigenetic processes involved in determining olfactory epithelial stem cell fate during injury-induced regeneration.
saseR: Juggling offsets unlocks RNA-seq tools for fast and Scalable differential usage, Aberrant Splicing and Expression Retrieval.
Abstract RNA-seq data analysis relies on many different tools, each tailored to specific applications and coming with unique assumptions and restrictions. Indeed, tools for differential transcript usage, or diagnosing patients with rare diseases through splicing and expression outliers, either lack in performance, discard information, or do not scale to massive data compendia.
Does sweetness exposure drive ‘sweet tooth’?
Core share and HTML view are not available for this content. However, as you have access to this content, a full PDF is available via the ‘Save PDF’ action button. It is widely believed that exposure to sweetened foods and beverages stimulates the liking and desire for sweetness.
Gastrointestinal tolerance of D-allulose in children: an acute, randomised, double-blind, placebo-controlled, cross-over study
Gastrointestinal tolerance of d-allulose in children: an acute, randomised, double-blind, placebo-controlled, cross-over study† D-Allulose, a low-calorie sugar, provides an attractive alternative to added sugars in food and beverage products. There is however limited data on its gastrointestinal (GI) tolerance, with only two studies in adults, and no studies in children to date.
Gastrointestinal tolerance of d-allulose in children: an acute, randomised, double-blind, placebo-controlled, cross-over study
Gastrointestinal tolerance of d-allulose in children: an acute, randomised, double-blind, placebo-controlled, cross-over study D-allulose, a low-calorie sugar, provides an attractive alternative to added sugars in food and beverage products. There is however limited data on its gastrointestinal (GI) tolerance, with only two studies in adults, and no studies in children to date.
A Latent Activated Olfactory Stem Cell State Revealed by Single Cell Transcriptomic and Epigenomic Profiling
Abstract The olfactory epithelium is one of the few regions of the nervous system that sustains neurogenesis throughout life. Its experimental accessibility makes it especially tractable for studying molecular mechanisms that drive neural regeneration after injury-induced cell death. In this study, we used single cell sequencing to identify major regulatory players in determining olfactory epithelial stem cell fate after acute injury.
Effect of industrial processing and storage procedures on oxysterols in milk and milk products
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Assessment of statistical methods from single cell, bulk RNA-seq, and metagenomics applied to microbiome data
Abstract Background The correct identification of differentially abundant microbial taxa between experimental conditions is a methodological and computational challenge. Recent work has produced methods to deal with the high sparsity and compositionality characteristic of microbiome data, but independent benchmarks comparing these to alternatives developed for RNA-seq data analysis are lacking.
Global diversity in the TAS2R38 bitter taste receptor: revisiting a classic evolutionary PROPosal
Davide S. Risso,a,1,2 Massimo Mezzavilla,3,4 Luca Pagani,2,5 Antonietta Robino,3 Gabriella Morini,6 Sergio Tofanelli,7 Maura Carrai,7 Daniele Campa,7 Roberto Barale,7 Fabio Caradonna,8 Paolo Gasparini,3 Donata Luiselli,2 Stephen Wooding,9 and Dennis Drayna1 Davide S.
An African-specific haplotype in MRGPRX4 is associated with menthol cigarette smoking
Loading metrics Open Access Peer-reviewed Research Article Julia Kozlitina , Davide Risso , Katherine Lansu, Reid Hans Johnson Olsen, Eduardo Sainz, Donata Luiselli, Arnab Barik, Carlos Frigerio-Domingues, Luca Pagani, Stephen Wooding, Thomas Kirchner, Ray Niaura, Bryan Roth, Dennis Drayna Julia Kozlitina, Davide Risso, Katherine Lansu, Reid Hans Johnson Olsen, Eduardo Sainz, Donata Luiselli, Arnab Barik, Carlos Frigerio-Domingues, Luca Pagani, Stephen Wooding Published: February 15, 2019...
Observation weights unlock bulk RNA-seq tools for zero inflation and single-cell applications
We argue that standard bulk RNA-seq methods for inferring differential gene expression suffer from zero inflation with respect to the assumed NB distribution when applied to scRNA-seq data. We propose instead modeling scRNA-seq data using a zero-inflated model and perform inference on the count component of the model, which is equivalent to standard NB regression where excess zeros are downweighted based on posterior probabilities (weights) inferred from a ZINB model.
Bioconductor workflow for single-cell RNA sequencing: Normalization, dimensionality reduction, clustering, and lineage inference
Here, we propose an integrated workflow for dowstream analysis, with the following four main steps: (1) dimensionality reduction accounting for zero inflation and over-dispersion, and adjusting for gene and cell-level covariates, using the zinbwave Bioconductor package; (2) robust and stable cell clustering using resampling-based sequential ensemble clustering, as implemented in the clusterExperiment Bioconductor package; (3) inference of cell lineages and ordering of the cells by...
Deficiency of microRNA miR-34a expands cell fate potential in pluripotent stem cells
Biological roles for microRNAs are not limited to RNA silencing and posttranscriptional regulation; they have now been shown to also regulate cell pluripotency. Choi et al. eliminated miR-34a from mouse embryonic stem cells and found that the cells exhibited a bidirectional cell fate potential, generating both embryonic and extraembryonic lineages (see the Perspective by Hasuwa and Siomi).
Deficiency of microRNA miR-34a expands cell fate potential in pluripotent stem cells
Embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs) efficiently generate all embryonic cell lineages, but rarely generate extra-embryonic cell types. We show that microRNA miR-34a deficiency expands the developmental potential of mouse pluripotent stem cells to yield both embryonic and extra-embryonic lineages and strongly induce MuERV-L (MERVL) endogenous retroviruses, similar to what is seen with totipotent 2-cell blastomeres.
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